Title: Visualize Draws from the Prior and Posterior Distributions
Description: Interactive visualization for Bayesian prior and posterior distributions.
When both distributions are provided the animation shows a transition from
prior to posterior. Finally, the animation splits the distribution using the provided
'breaks' into bars that show the probability for each region.
If no 'breaks' are providers it will use zero by default.
Author: Ignacio Martinez [aut, cre],
Linus Marco [aut],
Dan Thal [aut]
Maintainer: Ignacio Martinez <ignacio@protonmail.com>
Diff between vizdraws versions 1.0.0 dated 2020-04-28 and 1.1 dated 2021-01-08
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Title: Perform Inference on Algorithm-Agnostic Variable Importance
Description: Calculate point estimates of and valid confidence intervals for
nonparametric, algorithm-agnostic variable importance measures in high and low dimensions,
using flexible estimators of the underlying regression functions. For more information
about the methods, please see Williamson et al. (Biometrics, 2020), Williamson et al. (arXiv, 2020+) <arXiv:2004.03683>, and Williamson and Feng (ICML, 2020).
Author: Brian D. Williamson [aut, cre]
(<https://orcid.org/0000-0002-7024-548X>),
Jean Feng [ctb],
Noah Simon [ths] (<https://orcid.org/0000-0002-8985-2474>),
Marco Carone [ths] (<https://orcid.org/0000-0003-2106-0953>)
Maintainer: Brian D. Williamson <bwillia2@fredhutch.org>
Diff between vimp versions 2.1.0 dated 2020-06-18 and 2.1.6 dated 2021-01-08
vimp-2.1.0/vimp/R/cv_predictiveness_point_est.R |only vimp-2.1.0/vimp/R/cv_predictiveness_update.R |only vimp-2.1.0/vimp/R/cv_vimp_point_est.R |only vimp-2.1.0/vimp/R/cv_vimp_update.R |only vimp-2.1.0/vimp/R/predictiveness_ci.R |only vimp-2.1.0/vimp/R/predictiveness_point_est.R |only vimp-2.1.0/vimp/R/predictiveness_se.R |only vimp-2.1.0/vimp/R/predictiveness_update.R |only vimp-2.1.0/vimp/R/vimp_point_est.R |only vimp-2.1.0/vimp/R/vimp_update.R |only vimp-2.1.0/vimp/inst/doc/introduction_to_vimp.R |only vimp-2.1.0/vimp/inst/doc/introduction_to_vimp.Rmd |only vimp-2.1.0/vimp/inst/doc/introduction_to_vimp.html |only vimp-2.1.0/vimp/man/cv_predictiveness_point_est.Rd |only vimp-2.1.0/vimp/man/cv_predictiveness_update.Rd |only vimp-2.1.0/vimp/man/cv_vimp_point_est.Rd |only vimp-2.1.0/vimp/man/cv_vimp_update.Rd |only vimp-2.1.0/vimp/man/figures/vimp_logo.png |only vimp-2.1.0/vimp/man/predictiveness_ci.Rd |only vimp-2.1.0/vimp/man/predictiveness_point_est.Rd |only vimp-2.1.0/vimp/man/predictiveness_se.Rd |only vimp-2.1.0/vimp/man/predictiveness_update.Rd |only vimp-2.1.0/vimp/man/vimp_point_est.Rd |only vimp-2.1.0/vimp/man/vimp_update.Rd |only vimp-2.1.0/vimp/vignettes/introduction_to_vimp.Rmd |only vimp-2.1.6/vimp/DESCRIPTION | 31 - vimp-2.1.6/vimp/MD5 | 161 +++--- vimp-2.1.6/vimp/NAMESPACE | 21 vimp-2.1.6/vimp/NEWS.md | 81 +++ vimp-2.1.6/vimp/R/average_vim.R | 90 +-- vimp-2.1.6/vimp/R/cv_vim.R | 327 +++++++------- vimp-2.1.6/vimp/R/est_predictiveness.R |only vimp-2.1.6/vimp/R/est_predictiveness_cv.R |only vimp-2.1.6/vimp/R/format.vim.R | 27 - vimp-2.1.6/vimp/R/measure_accuracy.R | 40 + vimp-2.1.6/vimp/R/measure_anova.R |only vimp-2.1.6/vimp/R/measure_auc.R | 89 ++- vimp-2.1.6/vimp/R/measure_cross_entropy.R | 45 + vimp-2.1.6/vimp/R/measure_deviance.R | 58 +- vimp-2.1.6/vimp/R/measure_mse.R | 45 + vimp-2.1.6/vimp/R/measure_r_squared.R | 58 +- vimp-2.1.6/vimp/R/merge_vim.R | 54 -- vimp-2.1.6/vimp/R/print.vim.R | 9 vimp-2.1.6/vimp/R/sp_vim.R | 232 ++++++--- vimp-2.1.6/vimp/R/spvim_se.R | 2 vimp-2.1.6/vimp/R/utils.R | 124 ++++- vimp-2.1.6/vimp/R/vim.R | 249 +++++----- vimp-2.1.6/vimp/R/vimp-package.R | 19 vimp-2.1.6/vimp/R/vimp_accuracy.R | 28 - vimp-2.1.6/vimp/R/vimp_anova.R | 28 - vimp-2.1.6/vimp/R/vimp_auc.R | 28 - vimp-2.1.6/vimp/R/vimp_ci.R | 21 vimp-2.1.6/vimp/R/vimp_deviance.R | 30 - vimp-2.1.6/vimp/R/vimp_hypothesis_test.R | 75 --- vimp-2.1.6/vimp/R/vimp_regression.R | 30 - vimp-2.1.6/vimp/R/vimp_rsquared.R | 28 - vimp-2.1.6/vimp/R/vimp_se.R | 41 - vimp-2.1.6/vimp/R/zzz.R |only vimp-2.1.6/vimp/build/partial.rdb |only vimp-2.1.6/vimp/build/vignette.rds |binary vimp-2.1.6/vimp/inst/doc/introduction-to-vimp.R |only vimp-2.1.6/vimp/inst/doc/introduction-to-vimp.Rmd |only vimp-2.1.6/vimp/inst/doc/introduction-to-vimp.html |only vimp-2.1.6/vimp/inst/doc/precomputed-regressions.R |only vimp-2.1.6/vimp/inst/doc/precomputed-regressions.Rmd |only vimp-2.1.6/vimp/inst/doc/precomputed-regressions.html |only vimp-2.1.6/vimp/inst/doc/types-of-vims.R |only vimp-2.1.6/vimp/inst/doc/types-of-vims.Rmd |only vimp-2.1.6/vimp/inst/doc/types-of-vims.html |only vimp-2.1.6/vimp/man/average_vim.Rd | 18 vimp-2.1.6/vimp/man/cv_vim.Rd | 100 ++-- vimp-2.1.6/vimp/man/est_predictiveness.Rd |only vimp-2.1.6/vimp/man/est_predictiveness_cv.Rd |only vimp-2.1.6/vimp/man/figures/logo.png |only vimp-2.1.6/vimp/man/measure_accuracy.Rd | 35 + vimp-2.1.6/vimp/man/measure_anova.Rd |only vimp-2.1.6/vimp/man/measure_auc.Rd | 35 + vimp-2.1.6/vimp/man/measure_cross_entropy.Rd | 32 + vimp-2.1.6/vimp/man/measure_deviance.Rd | 35 + vimp-2.1.6/vimp/man/measure_mse.Rd | 35 + vimp-2.1.6/vimp/man/measure_r_squared.Rd | 39 + vimp-2.1.6/vimp/man/merge_vim.Rd | 20 vimp-2.1.6/vimp/man/sp_vim.Rd | 65 +- vimp-2.1.6/vimp/man/vim.Rd | 65 +- vimp-2.1.6/vimp/man/vimp.Rd | 21 vimp-2.1.6/vimp/man/vimp_accuracy.Rd | 34 - vimp-2.1.6/vimp/man/vimp_anova.Rd | 34 - vimp-2.1.6/vimp/man/vimp_auc.Rd | 34 - vimp-2.1.6/vimp/man/vimp_ci.Rd | 2 vimp-2.1.6/vimp/man/vimp_deviance.Rd | 34 - vimp-2.1.6/vimp/man/vimp_hypothesis_test.Rd | 35 - vimp-2.1.6/vimp/man/vimp_regression.Rd | 34 - vimp-2.1.6/vimp/man/vimp_rsquared.Rd | 36 - vimp-2.1.6/vimp/man/vimp_se.Rd | 15 vimp-2.1.6/vimp/tests/testthat/test-average_vim.R | 77 +-- vimp-2.1.6/vimp/tests/testthat/test-binary_outcomes.R | 90 ++- vimp-2.1.6/vimp/tests/testthat/test-continuous_outcomes.R | 50 +- vimp-2.1.6/vimp/tests/testthat/test-cv_vim.R | 130 +++-- vimp-2.1.6/vimp/tests/testthat/test-ipcw.R |only vimp-2.1.6/vimp/tests/testthat/test-merge_vim.R | 76 +-- vimp-2.1.6/vimp/tests/testthat/test-sp_vim.R | 80 ++- vimp-2.1.6/vimp/tests/testthat/test-vim.R | 109 ++-- vimp-2.1.6/vimp/vignettes/introduction-to-vimp.Rmd |only vimp-2.1.6/vimp/vignettes/precomputed-regressions.Rmd |only vimp-2.1.6/vimp/vignettes/types-of-vims.Rmd |only 105 files changed, 1998 insertions(+), 1443 deletions(-)
Title: Timescale-Specific Variance Ratio for Use in Community Ecology
Description: Tools for timescale decomposition of the classic variance ratio of community ecology. Tools are as described in Zhao et al (in prep), extending commonly used methods introduced by Peterson et al (1975) <doi: 10.2307/1936306>.
Author: Daniel C. Reuman [aut, cre],
Lei Zhao [aut],
Shaopeng Wang [aut]
Maintainer: Daniel C. Reuman <reuman@ku.edu>
Diff between tsvr versions 1.0.1 dated 2019-09-27 and 1.0.2 dated 2021-01-08
DESCRIPTION | 10 +++++----- MD5 | 13 +++++++------ inst/doc/tsvrvignette.R | 14 +++++++------- inst/doc/tsvrvignette.pdf |binary man/JRGdat.Rd | 6 ++++-- tests/testthat/helper-utils.R |only tests/testthat/tests_tsvreq_classic_methods.R | 2 +- tests/testthat/tests_tsvreq_methods.R | 2 +- 8 files changed, 25 insertions(+), 22 deletions(-)
Title: Feature Selection (Including Multiple Solutions) and Bayesian
Networks
Description: Many feature selection methods for a wide range of response variables, including minimal, statistically-equivalent and equally-predictive feature subsets. Bayesian network algorithms and related functions are also included. The package name 'MXM' stands for "Mens eX Machina", meaning "Mind from the Machine" in Latin. References: a) Lagani, V. and Athineou, G. and Farcomeni, A. and Tsagris, M. and Tsamardinos, I. (2017). Feature Selection with the R Package MXM: Discovering Statistically Equivalent Feature Subsets. Journal of Statistical Software, 80(7). <doi:10.18637/jss.v080.i07>. b) Tsagris, M., Lagani, V. and Tsamardinos, I. (2018). Feature selection for high-dimensional temporal data. BMC Bioinformatics, 19:17. <doi:10.1186/s12859-018-2023-7>. c) Tsagris, M., Borboudakis, G., Lagani, V. and Tsamardinos, I. (2018). Constraint-based causal discovery with mixed data. International Journal of Data Science and Analytics, 6(1): 19-30. <doi:10.1007/s41060-018-0097-y>. d) Tsagris, M., Papadovasilakis, Z., Lakiotaki, K. and Tsamardinos, I. (2018). Efficient feature selection on gene expression data: Which algorithm to use? BioRxiv. <doi:10.1101/431734>. e) Tsagris, M. (2019). Bayesian Network Learning with the PC Algorithm: An Improved and Correct Variation. Applied Artificial Intelligence, 33(2):101-123. <doi:10.1080/08839514.2018.1526760>. f) Tsagris, M. and Tsamardinos, I. (2019). Feature selection with the R package MXM. F1000Research 7: 1505. <doi:10.12688/f1000research.16216.2>. g) Borboudakis, G. and Tsamardinos, I. (2019). Forward-Backward Selection with Early Dropping. Journal of Machine Learning Research 20: 1-39. h) The gamma-OMP algorithm for feature selection with application to gene expression data. IEEE/ACM Transactions on Computational Biology and Bioinformatics (Accepted for publication).
Author: Michail Tsagris [aut, cre],
Ioannis Tsamardinos [aut, cph],
Vincenzo Lagani [aut, cph],
Giorgos Athineou [aut],
Giorgos Borboudakis [ctb],
Anna Roumpelaki [ctb]
Maintainer: Michail Tsagris <mtsagris@uoc.gr>
Diff between MXM versions 1.4.9 dated 2020-09-03 and 1.5.0 dated 2021-01-08
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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] (iSCAM functions)
Maintainer: Adrian Hordyk <adrian@bluematterscience.com>
Diff between MSEtool versions 2.0.1 dated 2020-09-29 and 3.0.0 dated 2021-01-08
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| 157 MSEtool-3.0.0/MSEtool/R/Awatea2OM.R | 336 - MSEtool-3.0.0/MSEtool/R/B_Low_functions.R |only MSEtool-3.0.0/MSEtool/R/Class_definitions.R |only MSEtool-3.0.0/MSEtool/R/DFO.R |only MSEtool-3.0.0/MSEtool/R/Data2csv.R |only MSEtool-3.0.0/MSEtool/R/Data_Functions.R |only MSEtool-3.0.0/MSEtool/R/Data_Plotting.R |only MSEtool-3.0.0/MSEtool/R/Data_documentation.r |only MSEtool-3.0.0/MSEtool/R/Data_make_update.R |only MSEtool-3.0.0/MSEtool/R/Fease_Functions.R |only MSEtool-3.0.0/MSEtool/R/MMSE_Object.r |only MSEtool-3.0.0/MSEtool/R/MMSE_plots.R | 291 - MSEtool-3.0.0/MSEtool/R/MOM_functions.R | 15 MSEtool-3.0.0/MSEtool/R/MOM_import.R |only MSEtool-3.0.0/MSEtool/R/MOM_object.r |only MSEtool-3.0.0/MSEtool/R/MPs_Reference.R |only MSEtool-3.0.0/MSEtool/R/MSC.R |only MSEtool-3.0.0/MSEtool/R/MSE_Plotting.R |only MSEtool-3.0.0/MSEtool/R/MSE_Plotting_PMs.R |only MSEtool-3.0.0/MSEtool/R/MSE_functions.R |only MSEtool-3.0.0/MSEtool/R/Misc_Exported.R |only MSEtool-3.0.0/MSEtool/R/Misc_Internal.R |only MSEtool-3.0.0/MSEtool/R/Movement_calcs.R | 144 MSEtool-3.0.0/MSEtool/R/OM_Plotting.R |only MSEtool-3.0.0/MSEtool/R/OM_functions.R |only MSEtool-3.0.0/MSEtool/R/OM_import.R |only MSEtool-3.0.0/MSEtool/R/OM_init_doc.R |only MSEtool-3.0.0/MSEtool/R/PMobjects.R |only MSEtool-3.0.0/MSEtool/R/PMtable.R |only MSEtool-3.0.0/MSEtool/R/ProjectMOM.R |only MSEtool-3.0.0/MSEtool/R/RcppExports.R |only MSEtool-3.0.0/MSEtool/R/SS2Data.R | 254 + MSEtool-3.0.0/MSEtool/R/SS2MOM.R | 118 MSEtool-3.0.0/MSEtool/R/SS2OM.R | 718 --- MSEtool-3.0.0/MSEtool/R/SSinternal.R | 857 ++-- MSEtool-3.0.0/MSEtool/R/SampleOM.R |only MSEtool-3.0.0/MSEtool/R/Sketch_Functions.R |only MSEtool-3.0.0/MSEtool/R/Turing.R |only MSEtool-3.0.0/MSEtool/R/VPA2OM.R | 49 MSEtool-3.0.0/MSEtool/R/aaImportFrom.R |only MSEtool-3.0.0/MSEtool/R/applyMMP.R | 103 MSEtool-3.0.0/MSEtool/R/iSCAM2OM.R | 527 -- MSEtool-3.0.0/MSEtool/R/multiMSE.R | 3017 ++++++++------- MSEtool-3.0.0/MSEtool/R/multiMSE_internal.R | 336 - MSEtool-3.0.0/MSEtool/R/multi_q_estimation.R | 188 MSEtool-3.0.0/MSEtool/R/popdyn.R |only MSEtool-3.0.0/MSEtool/R/popdyn_MICE.R | 282 - MSEtool-3.0.0/MSEtool/R/runMSE.R |only MSEtool-3.0.0/MSEtool/R/sysdata.rda |only MSEtool-3.0.0/MSEtool/R/utils.R |only MSEtool-3.0.0/MSEtool/README.md | 40 MSEtool-3.0.0/MSEtool/data/Albacore.rda |only MSEtool-3.0.0/MSEtool/data/Albacore_TwoFleet.rda |binary MSEtool-3.0.0/MSEtool/data/Atlantic_mackerel.rda |only MSEtool-3.0.0/MSEtool/data/Blue_shark.rda |only MSEtool-3.0.0/MSEtool/data/Bluefin_tuna.rda |only MSEtool-3.0.0/MSEtool/data/Bluefin_tuna_WAtl.rda |only MSEtool-3.0.0/MSEtool/data/Butterfish.rda |only MSEtool-3.0.0/MSEtool/data/China_rockfish.rda |only MSEtool-3.0.0/MSEtool/data/Cobia.rda |only MSEtool-3.0.0/MSEtool/data/DataDescription.rda |only MSEtool-3.0.0/MSEtool/data/DataSlots.rda |only MSEtool-3.0.0/MSEtool/data/DecE_Dom.rda |only MSEtool-3.0.0/MSEtool/data/DecE_HDom.rda |only MSEtool-3.0.0/MSEtool/data/DecE_NDom.rda |only MSEtool-3.0.0/MSEtool/data/Example_datafile.rda |only MSEtool-3.0.0/MSEtool/data/FlatE_Dom.rda |only MSEtool-3.0.0/MSEtool/data/FlatE_HDom.rda |only MSEtool-3.0.0/MSEtool/data/FlatE_NDom.rda |only MSEtool-3.0.0/MSEtool/data/FleetDescription.rda |only MSEtool-3.0.0/MSEtool/data/Generic_DecE.rda |only MSEtool-3.0.0/MSEtool/data/Generic_FlatE.rda |only MSEtool-3.0.0/MSEtool/data/Generic_Fleet.rda |only MSEtool-3.0.0/MSEtool/data/Generic_IncE.rda |only MSEtool-3.0.0/MSEtool/data/Generic_Obs.rda |only MSEtool-3.0.0/MSEtool/data/Gulf_blue_tilefish.rda |only MSEtool-3.0.0/MSEtool/data/Herring.rda |only MSEtool-3.0.0/MSEtool/data/ImpDescription.rda |only MSEtool-3.0.0/MSEtool/data/Imprecise_Biased.rda |only MSEtool-3.0.0/MSEtool/data/Imprecise_Unbiased.rda |only MSEtool-3.0.0/MSEtool/data/IncE_HDom.rda |only MSEtool-3.0.0/MSEtool/data/IncE_NDom.rda |only MSEtool-3.0.0/MSEtool/data/LHdatabase.rda |only MSEtool-3.0.0/MSEtool/data/Low_Effort_Non_Target.rda |only MSEtool-3.0.0/MSEtool/data/MSEDescription.rda |only MSEtool-3.0.0/MSEtool/data/Mackerel.rda |only MSEtool-3.0.0/MSEtool/data/OMDescription.rda |only MSEtool-3.0.0/MSEtool/data/ObsDescription.rda |only MSEtool-3.0.0/MSEtool/data/Overages.rda |only MSEtool-3.0.0/MSEtool/data/Perfect_Imp.rda |only MSEtool-3.0.0/MSEtool/data/Perfect_Info.rda |only MSEtool-3.0.0/MSEtool/data/Porgy.rda |only MSEtool-3.0.0/MSEtool/data/Precise_Biased.rda |only MSEtool-3.0.0/MSEtool/data/Precise_Unbiased.rda |only MSEtool-3.0.0/MSEtool/data/Red_snapper.rda |only MSEtool-3.0.0/MSEtool/data/ReqData.rda |only MSEtool-3.0.0/MSEtool/data/Rockfish.rda |only MSEtool-3.0.0/MSEtool/data/SimulatedData.rda |only MSEtool-3.0.0/MSEtool/data/Simulation_1.rda |only MSEtool-3.0.0/MSEtool/data/Snapper.rda |only MSEtool-3.0.0/MSEtool/data/Sole.rda |only MSEtool-3.0.0/MSEtool/data/StockDescription.rda |only MSEtool-3.0.0/MSEtool/data/Target_All_Fish.rda |only MSEtool-3.0.0/MSEtool/data/Targeting_Small_Fish.rda |only MSEtool-3.0.0/MSEtool/data/Toothfish.rda |only MSEtool-3.0.0/MSEtool/data/ourReefFish.rda |only MSEtool-3.0.0/MSEtool/data/testOM.rda |only MSEtool-3.0.0/MSEtool/inst/Data.csv |only MSEtool-3.0.0/MSEtool/inst/Data.xlsx |only MSEtool-3.0.0/MSEtool/inst/Example_Chile_Hake.rmd |only MSEtool-3.0.0/MSEtool/inst/Example_Chile_Hake.xlsx |only MSEtool-3.0.0/MSEtool/inst/OM.rmd |only MSEtool-3.0.0/MSEtool/inst/OM.xlsx |only MSEtool-3.0.0/MSEtool/inst/Rmd |only MSEtool-3.0.0/MSEtool/man/BlankSelPlot.Rd |only MSEtool-3.0.0/MSEtool/man/Blow_opt.Rd |only MSEtool-3.0.0/MSEtool/man/CALsimp.Rd |only MSEtool-3.0.0/MSEtool/man/CSRA.Rd |only MSEtool-3.0.0/MSEtool/man/CSRAfunc.Rd |only MSEtool-3.0.0/MSEtool/man/CalcMPDynamics.Rd |only MSEtool-3.0.0/MSEtool/man/CalculateQ.Rd |only MSEtool-3.0.0/MSEtool/man/Can.Rd |only MSEtool-3.0.0/MSEtool/man/CheckDuplicate.Rd |only MSEtool-3.0.0/MSEtool/man/CheckMPs.Rd |only MSEtool-3.0.0/MSEtool/man/ChkYrs.Rd |only MSEtool-3.0.0/MSEtool/man/Choose.Rd |only MSEtool-3.0.0/MSEtool/man/CombineMMP.Rd |only MSEtool-3.0.0/MSEtool/man/Converge.Rd |only MSEtool-3.0.0/MSEtool/man/Cos_thresh_tab.Rd |only MSEtool-3.0.0/MSEtool/man/Cplot.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_bar.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_hist.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_plot.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_plot2.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_proj.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_quant.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_report.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_spider.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_tab.Rd |only MSEtool-3.0.0/MSEtool/man/DFO_tab_formatted.Rd |only MSEtool-3.0.0/MSEtool/man/DLMDataDir.Rd |only MSEtool-3.0.0/MSEtool/man/Data-class-objects.Rd |only MSEtool-3.0.0/MSEtool/man/Data-class.Rd |only MSEtool-3.0.0/MSEtool/man/Data2csv.Rd |only MSEtool-3.0.0/MSEtool/man/DataDescription.Rd |only MSEtool-3.0.0/MSEtool/man/DataDir.Rd |only MSEtool-3.0.0/MSEtool/man/DataInit.Rd |only MSEtool-3.0.0/MSEtool/man/DataSlots.Rd |only MSEtool-3.0.0/MSEtool/man/Data_xl.Rd |only MSEtool-3.0.0/MSEtool/man/Dom.Rd |only MSEtool-3.0.0/MSEtool/man/FMSYref.Rd |only MSEtool-3.0.0/MSEtool/man/Fease.Rd |only MSEtool-3.0.0/MSEtool/man/Fleet-class-objects.Rd |only MSEtool-3.0.0/MSEtool/man/Fleet-class.Rd |only MSEtool-3.0.0/MSEtool/man/FleetDescription.Rd |only MSEtool-3.0.0/MSEtool/man/GenerateRandomWalk.Rd |only MSEtool-3.0.0/MSEtool/man/Hist-class.Rd |only MSEtool-3.0.0/MSEtool/man/HistMICE.Rd | 21 MSEtool-3.0.0/MSEtool/man/Imp-class-objects.Rd |only MSEtool-3.0.0/MSEtool/man/Imp-class.Rd |only MSEtool-3.0.0/MSEtool/man/ImpDescription.Rd |only MSEtool-3.0.0/MSEtool/man/Input.Rd |only MSEtool-3.0.0/MSEtool/man/Kplot.Rd |only MSEtool-3.0.0/MSEtool/man/L2A.Rd |only MSEtool-3.0.0/MSEtool/man/LH2OM.Rd |only MSEtool-3.0.0/MSEtool/man/LHdatabase.Rd |only MSEtool-3.0.0/MSEtool/man/LinInterp.Rd |only MSEtool-3.0.0/MSEtool/man/ML2D.Rd |only MSEtool-3.0.0/MSEtool/man/MMSE-class.Rd | 198 MSEtool-3.0.0/MSEtool/man/MOM-class-objects.Rd |only MSEtool-3.0.0/MSEtool/man/MOM-class.Rd | 4 MSEtool-3.0.0/MSEtool/man/MPCalcsNAs.Rd | 34 MSEtool-3.0.0/MSEtool/man/MPtype.Rd |only MSEtool-3.0.0/MSEtool/man/MPurl.Rd |only MSEtool-3.0.0/MSEtool/man/MSE-class.Rd |only MSEtool-3.0.0/MSEtool/man/MSEDescription.Rd |only MSEtool-3.0.0/MSEtool/man/MSEextra.Rd |only MSEtool-3.0.0/MSEtool/man/MSYCalcs.Rd |only MSEtool-3.0.0/MSEtool/man/NAor0.Rd |only MSEtool-3.0.0/MSEtool/man/NOAA_plot.Rd |only MSEtool-3.0.0/MSEtool/man/OM-class-objects.Rd |only MSEtool-3.0.0/MSEtool/man/OM-class.Rd |only MSEtool-3.0.0/MSEtool/man/OMDescription.Rd |only MSEtool-3.0.0/MSEtool/man/OMdoc.Rd |only MSEtool-3.0.0/MSEtool/man/OMexample.Rd |only MSEtool-3.0.0/MSEtool/man/OMinit.Rd |only MSEtool-3.0.0/MSEtool/man/Obs-class-objects.Rd |only MSEtool-3.0.0/MSEtool/man/Obs-class.Rd |only MSEtool-3.0.0/MSEtool/man/ObsDescription.Rd |only MSEtool-3.0.0/MSEtool/man/OneRep.Rd |only MSEtool-3.0.0/MSEtool/man/PMLimit.Rd |only MSEtool-3.0.0/MSEtool/man/PMobj-class.Rd |only MSEtool-3.0.0/MSEtool/man/PWhisker.Rd |only MSEtool-3.0.0/MSEtool/man/PerformanceMetric.Rd |only MSEtool-3.0.0/MSEtool/man/Pplot.Rd |only MSEtool-3.0.0/MSEtool/man/Pplot2.Rd |only MSEtool-3.0.0/MSEtool/man/Range.Rd |only MSEtool-3.0.0/MSEtool/man/RealFease.Rd |only MSEtool-3.0.0/MSEtool/man/Rec-class.Rd |only MSEtool-3.0.0/MSEtool/man/Replace.Rd |only MSEtool-3.0.0/MSEtool/man/Report.Rd |only MSEtool-3.0.0/MSEtool/man/ReqData.Rd |only MSEtool-3.0.0/MSEtool/man/Required.Rd |only MSEtool-3.0.0/MSEtool/man/ResFromRel.Rd | 48 MSEtool-3.0.0/MSEtool/man/SIL.Rd | 38 MSEtool-3.0.0/MSEtool/man/SS2Data.Rd | 7 MSEtool-3.0.0/MSEtool/man/SS2DataMOM.Rd |only MSEtool-3.0.0/MSEtool/man/SS2MOM.Rd | 91 MSEtool-3.0.0/MSEtool/man/SSBrefplot.Rd |only MSEtool-3.0.0/MSEtool/man/SampleCpars.Rd |only MSEtool-3.0.0/MSEtool/man/SampleFleetPars.Rd |only MSEtool-3.0.0/MSEtool/man/SampleImpPars.Rd |only MSEtool-3.0.0/MSEtool/man/SampleObsPars.Rd |only MSEtool-3.0.0/MSEtool/man/SampleStockPars.Rd |only MSEtool-3.0.0/MSEtool/man/Sense.Rd |only MSEtool-3.0.0/MSEtool/man/SimulatedData.Rd |only MSEtool-3.0.0/MSEtool/man/SketchFun.Rd |only MSEtool-3.0.0/MSEtool/man/Stock-class-objects.Rd |only MSEtool-3.0.0/MSEtool/man/Stock-class.Rd |only MSEtool-3.0.0/MSEtool/man/StockDescription.Rd |only MSEtool-3.0.0/MSEtool/man/Sub.Rd |only MSEtool-3.0.0/MSEtool/man/SubCpars.Rd |only MSEtool-3.0.0/MSEtool/man/SubOM.Rd |only MSEtool-3.0.0/MSEtool/man/TAC.Rd |only MSEtool-3.0.0/MSEtool/man/TACfilter.Rd |only MSEtool-3.0.0/MSEtool/man/TEG.Rd | 34 MSEtool-3.0.0/MSEtool/man/Thresh_tab.Rd |only MSEtool-3.0.0/MSEtool/man/TradePlot.Rd |only MSEtool-3.0.0/MSEtool/man/Turing.Rd |only MSEtool-3.0.0/MSEtool/man/Uses.Rd |only MSEtool-3.0.0/MSEtool/man/VOI.Rd |only MSEtool-3.0.0/MSEtool/man/VOI2.Rd |only MSEtool-3.0.0/MSEtool/man/VOIplot.Rd |only MSEtool-3.0.0/MSEtool/man/VPA2OM.Rd | 174 MSEtool-3.0.0/MSEtool/man/XL2Data.Rd |only MSEtool-3.0.0/MSEtool/man/XL2Fleet.Rd |only MSEtool-3.0.0/MSEtool/man/XL2OM.Rd |only MSEtool-3.0.0/MSEtool/man/XL2Stock.Rd |only MSEtool-3.0.0/MSEtool/man/alphaconv.Rd |only MSEtool-3.0.0/MSEtool/man/applyMMP.Rd |only MSEtool-3.0.0/MSEtool/man/applyMP.Rd |only MSEtool-3.0.0/MSEtool/man/avail.Rd | 67 MSEtool-3.0.0/MSEtool/man/boxplot.Data.Rd |only MSEtool-3.0.0/MSEtool/man/calcMean.Rd |only MSEtool-3.0.0/MSEtool/man/calcProb.Rd |only MSEtool-3.0.0/MSEtool/man/calcRefYield.Rd |only MSEtool-3.0.0/MSEtool/man/char.log-class.Rd |only MSEtool-3.0.0/MSEtool/man/checkMSE.Rd |only MSEtool-3.0.0/MSEtool/man/cparscheck.Rd |only MSEtool-3.0.0/MSEtool/man/cv.Rd |only MSEtool-3.0.0/MSEtool/man/dnormal.Rd |only MSEtool-3.0.0/MSEtool/man/genSizeCompWrap.Rd |only MSEtool-3.0.0/MSEtool/man/getAFC.Rd |only MSEtool-3.0.0/MSEtool/man/getBlow.Rd |only MSEtool-3.0.0/MSEtool/man/getDataList.Rd |only MSEtool-3.0.0/MSEtool/man/getEffhist.Rd |only MSEtool-3.0.0/MSEtool/man/getclass.Rd |only MSEtool-3.0.0/MSEtool/man/getfirstlev.Rd |only MSEtool-3.0.0/MSEtool/man/getmov2.Rd |only MSEtool-3.0.0/MSEtool/man/getq_multi_MICE.Rd | 29 MSEtool-3.0.0/MSEtool/man/getsel.Rd |only MSEtool-3.0.0/MSEtool/man/hist2.Rd |only MSEtool-3.0.0/MSEtool/man/hrate.Rd | 36 MSEtool-3.0.0/MSEtool/man/iSCAM2Data.Rd | 2 MSEtool-3.0.0/MSEtool/man/iSCAM2OM.Rd | 99 MSEtool-3.0.0/MSEtool/man/iSCAMcomps.Rd | 44 MSEtool-3.0.0/MSEtool/man/iSCAMinds.Rd | 54 MSEtool-3.0.0/MSEtool/man/initialize-methods.Rd |only MSEtool-3.0.0/MSEtool/man/joinData.Rd |only MSEtool-3.0.0/MSEtool/man/join_plots.Rd |only MSEtool-3.0.0/MSEtool/man/label.class-class.Rd |only MSEtool-3.0.0/MSEtool/man/ldim.Rd | 34 MSEtool-3.0.0/MSEtool/man/load.iscam.files.Rd | 50 MSEtool-3.0.0/MSEtool/man/makeTransparent.Rd |only MSEtool-3.0.0/MSEtool/man/makemov.Rd | 46 MSEtool-3.0.0/MSEtool/man/movestockCPP.Rd |only MSEtool-3.0.0/MSEtool/man/movfit_Rcpp.Rd |only MSEtool-3.0.0/MSEtool/man/multiData.Rd | 2 MSEtool-3.0.0/MSEtool/man/multiDataS.Rd | 54 MSEtool-3.0.0/MSEtool/man/multiMSE.Rd | 94 MSEtool-3.0.0/MSEtool/man/multidebug.Rd | 54 MSEtool-3.0.0/MSEtool/man/optCPU.Rd |only MSEtool-3.0.0/MSEtool/man/optMSY_eq.Rd |only MSEtool-3.0.0/MSEtool/man/optQ.Rd |only MSEtool-3.0.0/MSEtool/man/optYield.Rd |only MSEtool-3.0.0/MSEtool/man/plot.Data.Rd |only MSEtool-3.0.0/MSEtool/man/plot.MMSE.Rd | 13 MSEtool-3.0.0/MSEtool/man/plot.MSE.Rd |only MSEtool-3.0.0/MSEtool/man/plot.Stock.Rd |only MSEtool-3.0.0/MSEtool/man/plotFun.Rd |only MSEtool-3.0.0/MSEtool/man/plotOFL.Rd |only MSEtool-3.0.0/MSEtool/man/plotmulti.Rd | 38 MSEtool-3.0.0/MSEtool/man/plotquant.Rd | 2 MSEtool-3.0.0/MSEtool/man/popdynCPP.Rd |only MSEtool-3.0.0/MSEtool/man/popdynMICE.Rd | 57 MSEtool-3.0.0/MSEtool/man/popdynOneMICE.Rd | 60 MSEtool-3.0.0/MSEtool/man/popdynOneTScpp.Rd |only MSEtool-3.0.0/MSEtool/man/prob.class-class.Rd |only MSEtool-3.0.0/MSEtool/man/qestMICE.Rd | 56 MSEtool-3.0.0/MSEtool/man/replic8.Rd |only MSEtool-3.0.0/MSEtool/man/runCOSEWIC.Rd |only MSEtool-3.0.0/MSEtool/man/runInMP.Rd |only MSEtool-3.0.0/MSEtool/man/runMP.Rd |only MSEtool-3.0.0/MSEtool/man/runMSE.Rd |only MSEtool-3.0.0/MSEtool/man/sample_steepness2.Rd |only MSEtool-3.0.0/MSEtool/man/sdconv.Rd |only MSEtool-3.0.0/MSEtool/man/setup.Rd |only MSEtool-3.0.0/MSEtool/man/show-MSE.Rd |only MSEtool-3.0.0/MSEtool/man/show-Rec.Rd |only MSEtool-3.0.0/MSEtool/man/simCAA.Rd |only MSEtool-3.0.0/MSEtool/man/simCAL.Rd |only MSEtool-3.0.0/MSEtool/man/simmov.Rd | 30 MSEtool-3.0.0/MSEtool/man/summary-Data.Rd |only MSEtool-3.0.0/MSEtool/man/summary-MSE.Rd |only MSEtool-3.0.0/MSEtool/man/tinyErr.Rd | 41 MSEtool-3.0.0/MSEtool/man/trlnorm.Rd |only MSEtool-3.0.0/MSEtool/man/validcpars.Rd |only MSEtool-3.0.0/MSEtool/man/wormplot.Rd |only MSEtool-3.0.0/MSEtool/man/writeCSV.Rd |only MSEtool-3.0.0/MSEtool/src/RcppExports.cpp |only MSEtool-3.0.0/MSEtool/src/genLenComp.cpp |only MSEtool-3.0.0/MSEtool/src/grav.cpp |only MSEtool-3.0.0/MSEtool/src/movefit_Rcpp.cpp |only MSEtool-3.0.0/MSEtool/src/popddynCPP.cpp |only MSEtool-3.0.0/MSEtool/tests |only 433 files changed, 5356 insertions(+), 4708 deletions(-)
Title: Miscellaneous Functions for Data Cleaning and Analysis
Description: Provides functions needed for data cleaning and
formatting and forms data cleaning and wrangling backend for the
following packages: 'broomExtra', 'ggstatsplot', 'groupedstats',
'pairwiseComparisons', 'statsExpressions', and 'tidyBF'.
Author: Indrajeet Patil [aut, cre, cph]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between ipmisc versions 5.0.1 dated 2020-12-08 and 5.0.2 dated 2021-01-08
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NAMESPACE | 8 -------- NEWS.md | 4 ++++ R/reexports.R | 18 ------------------ man/reexports.Rd | 6 ------ 6 files changed, 13 insertions(+), 41 deletions(-)
Title: Sample Size Calculation for the Comparison of Means or
Proportions in Phase III Clinical Trials
Description: There are four categories of Phase III clinical trials according to different research goals, including (1) Testing for equality, (2) Superiority trial, (3) Non-inferiority trial, and (4) Equivalence trial. This package aims to help researchers to calculate sample size when comparing means or proportions in Phase III clinical trials with different research goals.
Author: Hongchao Qi, Fang Zhu
Maintainer: Hongchao Qi <hcqi1992@gmail.com>
Diff between SampleSize4ClinicalTrials versions 0.2.2 dated 2020-03-25 and 0.2.3 dated 2021-01-08
DESCRIPTION | 10 +++++----- MD5 | 4 ++-- man/SampleSize4ClinicalTrials.Rd | 1 - 3 files changed, 7 insertions(+), 8 deletions(-)
More information about SampleSize4ClinicalTrials at CRAN
Permanent link
Title: Tidyverse-Friendly Introductory Linear Regression
Description: Datasets and wrapper functions for tidyverse-friendly introductory linear regression, used in "Statistical Inference via Data Science: A ModernDive into R and the Tidyverse" available at <https://moderndive.com/>.
Author: Albert Y. Kim [aut, cre] (<https://orcid.org/0000-0001-7824-306X>),
Chester Ismay [aut] (<https://orcid.org/0000-0003-2820-2547>),
Andrew Bray [ctb] (<https://orcid.org/0000-0002-4037-7414>),
Delaney Moran [ctb],
Evgeni Chasnovski [ctb] (<https://orcid.org/0000-0002-1617-4019>),
Will Hopper [ctb] (<https://orcid.org/0000-0002-7848-1946>),
Marium Tapal [ctb] (<https://orcid.org/0000-0001-5093-6462>)
Maintainer: Albert Y. Kim <albert.ys.kim@gmail.com>
Diff between moderndive versions 0.5.0 dated 2020-07-19 and 0.5.1 dated 2021-01-08
DESCRIPTION | 16 +++++++------- MD5 | 25 +++++++++++++--------- NEWS.md | 10 +++++++++ build/vignette.rds |binary inst/doc/why-moderndive.R | 4 +-- inst/doc/why-moderndive.Rmd | 11 +++++++-- inst/doc/why-moderndive.html | 30 ++++++++++++++++++--------- tests/testthat/helper-utils.R |only tests/testthat/test-geom_parallel_slopes.R | 26 +++++++++++------------ tests/testthat/test_geom_categorical_model.R | 12 +++++----- vignettes/README.md |only vignettes/_build.sh |only vignettes/paper.bib | 2 - vignettes/paper.md |only vignettes/paper.pdf |only vignettes/why-moderndive.Rmd | 11 +++++++-- 16 files changed, 91 insertions(+), 56 deletions(-)
Title: Generate Postestimation Quantities for Bayesian MCMC Estimation
Description: An implementation of functions to generate and plot postestimation quantities after estimating Bayesian regression models using Markov chain Monte Carlo (MCMC). Functionality includes the estimation of the Precision-Recall curves (see Beger, 2016 <doi:10.2139/ssrn.2765419>), the implementation of the observed values method of calculating predicted probabilities by Hanmer and Kalkan (2013) <doi:10.1111/j.1540-5907.2012.00602.x>, the implementation of the average value method of calculating predicted probabilities (see King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>), and the generation and plotting of first differences to summarize typical effects across covariates (see Long 1997, ISBN:9780803973749; King, Tomz, and Wittenberg, 2000 <doi:10.2307/2669316>). This package can be used with MCMC output generated by any Bayesian estimation tool including 'JAGS', 'BUGS', 'MCMCpack', and 'Stan'.
Author: Johannes Karreth [aut] (<https://orcid.org/0000-0003-4586-7153>),
Shana Scogin [aut, cre] (<https://orcid.org/0000-0002-7801-853X>),
Rob Williams [aut] (<https://orcid.org/0000-0001-9259-3883>),
Andreas Beger [aut] (<https://orcid.org/0000-0003-1883-3169>),
Myunghee Lee [ctb],
Neil Williams [ctb]
Maintainer: Shana Scogin <shanarscogin@gmail.com>
Diff between BayesPostEst versions 0.2.1 dated 2020-05-28 and 0.3.1 dated 2021-01-08
BayesPostEst-0.2.1/BayesPostEst/R/mcmcFDplot.R |only BayesPostEst-0.2.1/BayesPostEst/man/mcmcFDplot.Rd |only BayesPostEst-0.2.1/BayesPostEst/tests/testthat/test_mcmcFD_mcmcFDplot.R |only BayesPostEst-0.2.1/BayesPostEst/vignettes/mod.rds |only BayesPostEst-0.3.1/BayesPostEst/DESCRIPTION | 20 BayesPostEst-0.3.1/BayesPostEst/MD5 | 116 BayesPostEst-0.3.1/BayesPostEst/NAMESPACE | 16 BayesPostEst-0.3.1/BayesPostEst/NEWS.md | 20 BayesPostEst-0.3.1/BayesPostEst/R/BayesPostEst-deprecated.R |only BayesPostEst-0.3.1/BayesPostEst/R/BayesPostEst.R | 38 BayesPostEst-0.3.1/BayesPostEst/R/data.R | 11 BayesPostEst-0.3.1/BayesPostEst/R/mcmcAveProb.R | 6 BayesPostEst-0.3.1/BayesPostEst/R/mcmcCoefPlot.R | 10 BayesPostEst-0.3.1/BayesPostEst/R/mcmcFD.R | 387 + BayesPostEst-0.3.1/BayesPostEst/R/mcmcMargEff.R | 4 BayesPostEst-0.3.1/BayesPostEst/R/mcmcObsProb.R | 6 BayesPostEst-0.3.1/BayesPostEst/R/mcmcReg.R | 159 BayesPostEst-0.3.1/BayesPostEst/R/mcmcRocPrc-methods.R |only BayesPostEst-0.3.1/BayesPostEst/R/mcmcRocPrc.R | 473 ++ BayesPostEst-0.3.1/BayesPostEst/R/mcmcRocPrcGen.R | 8 BayesPostEst-0.3.1/BayesPostEst/README.md | 789 ++-- BayesPostEst-0.3.1/BayesPostEst/build/partial.rdb |only BayesPostEst-0.3.1/BayesPostEst/build/vignette.rds |binary BayesPostEst-0.3.1/BayesPostEst/data/sim_data.rda |binary BayesPostEst-0.3.1/BayesPostEst/data/sim_data_interactive.rda |binary BayesPostEst-0.3.1/BayesPostEst/data/sim_data_interactive_cat.rda |binary BayesPostEst-0.3.1/BayesPostEst/inst/doc/getting_started.R | 251 - BayesPostEst-0.3.1/BayesPostEst/inst/doc/getting_started.Rmd | 88 BayesPostEst-0.3.1/BayesPostEst/inst/doc/getting_started.html | 1943 +++++----- BayesPostEst-0.3.1/BayesPostEst/man/BayesPostEst-deprecated.Rd |only BayesPostEst-0.3.1/BayesPostEst/man/BayesPostEst.Rd | 33 BayesPostEst-0.3.1/BayesPostEst/man/compute_roc.Rd |only BayesPostEst-0.3.1/BayesPostEst/man/identify_link_function.Rd |only BayesPostEst-0.3.1/BayesPostEst/man/is_binary_model.Rd |only BayesPostEst-0.3.1/BayesPostEst/man/jags_interactive.Rd | 6 BayesPostEst-0.3.1/BayesPostEst/man/jags_interactive_cat.Rd | 6 BayesPostEst-0.3.1/BayesPostEst/man/jags_logit.Rd | 6 BayesPostEst-0.3.1/BayesPostEst/man/jags_probit.Rd | 6 BayesPostEst-0.3.1/BayesPostEst/man/mcmcAveProb.Rd | 18 BayesPostEst-0.3.1/BayesPostEst/man/mcmcCoefPlot.Rd | 18 BayesPostEst-0.3.1/BayesPostEst/man/mcmcFD.Rd | 25 BayesPostEst-0.3.1/BayesPostEst/man/mcmcMargEff.Rd | 20 BayesPostEst-0.3.1/BayesPostEst/man/mcmcObsProb.Rd | 18 BayesPostEst-0.3.1/BayesPostEst/man/mcmcReg.Rd | 62 BayesPostEst-0.3.1/BayesPostEst/man/mcmcRocPrc.Rd | 189 BayesPostEst-0.3.1/BayesPostEst/man/mcmcRocPrcGen.Rd | 18 BayesPostEst-0.3.1/BayesPostEst/man/mcmcTab.Rd | 10 BayesPostEst-0.3.1/BayesPostEst/man/new_mcmcRocPrc.Rd |only BayesPostEst-0.3.1/BayesPostEst/man/plot.mcmcFD.Rd |only BayesPostEst-0.3.1/BayesPostEst/man/sim_data.Rd | 4 BayesPostEst-0.3.1/BayesPostEst/man/sim_data_interactive.Rd | 4 BayesPostEst-0.3.1/BayesPostEst/man/sim_data_interactive_cat.Rd | 4 BayesPostEst-0.3.1/BayesPostEst/tests/testdata |only BayesPostEst-0.3.1/BayesPostEst/tests/testdata-raw |only BayesPostEst-0.3.1/BayesPostEst/tests/testthat/helper-libs.R |only BayesPostEst-0.3.1/BayesPostEst/tests/testthat/test_mcmcAveProb.R | 1 BayesPostEst-0.3.1/BayesPostEst/tests/testthat/test_mcmcCoefPlot.R | 109 BayesPostEst-0.3.1/BayesPostEst/tests/testthat/test_mcmcFD.R |only BayesPostEst-0.3.1/BayesPostEst/tests/testthat/test_mcmcReg.R | 170 BayesPostEst-0.3.1/BayesPostEst/tests/testthat/test_mcmcRocPrc.R | 489 ++ BayesPostEst-0.3.1/BayesPostEst/tests/testthat/test_mcmcTab.R | 67 BayesPostEst-0.3.1/BayesPostEst/vignettes/getting_started.Rmd | 88 BayesPostEst-0.3.1/BayesPostEst/vignettes/references.bib | 24 63 files changed, 4108 insertions(+), 1632 deletions(-)
Title: Bayesian Spatial Split Population Survival Model
Description: Parametric spatial split-population (SP) survival models for clustered
event processes. The models account for structural and spatial heterogeneity among
“at risk” and “immune” populations, and incorporate time-varying covariates.
This package currently implements Weibull, Exponential and Log-logistic forms for
the duration component. It also includes functions for a series of diagnostic
tests and plots to easily visualize spatial autocorrelation, convergence, and spatial effects. Users can
create their own spatial weights matrix based on their units and adjacencies of
interest, making the use of these models flexible and broadly applicable to a
variety of research areas. Joo et al. (2020) <https://github.com/Nicolas-Schmidt/BayesSPsurv/blob/master/man/figures/SPcure.pdf> describe
the estimators included in this package.
Author: Brandon L. Bolte [aut],
Nicolas Schmidt [aut, cre],
Sergio Bejar [aut],
Bumba Mukherjee [aut],
Minnie M. Joo [ctb],
Nguyen K. Huynh [ctb]
Maintainer: Nicolas Schmidt <nschmidt@cienciassociales.edu.uy>
Diff between BayesSPsurv versions 0.1.1 dated 2020-11-25 and 0.1.2 dated 2021-01-08
BayesSPsurv-0.1.1/BayesSPsurv/man/plot_JointCount.Rd |only BayesSPsurv-0.1.2/BayesSPsurv/DESCRIPTION | 6 BayesSPsurv-0.1.2/BayesSPsurv/MD5 | 34 +- BayesSPsurv-0.1.2/BayesSPsurv/NAMESPACE | 2 BayesSPsurv-0.1.2/BayesSPsurv/NEWS.md | 11 BayesSPsurv-0.1.2/BayesSPsurv/R/exchangeSPsurv.R | 15 BayesSPsurv-0.1.2/BayesSPsurv/R/plots.R | 21 - BayesSPsurv-0.1.2/BayesSPsurv/R/pooledSPsurv.R | 15 BayesSPsurv-0.1.2/BayesSPsurv/R/spatialSPsurv.R | 19 - BayesSPsurv-0.1.2/BayesSPsurv/R/spatial_SA.R | 2 BayesSPsurv-0.1.2/BayesSPsurv/R/utils.R | 4 BayesSPsurv-0.1.2/BayesSPsurv/README.md | 155 ++++++++-- BayesSPsurv-0.1.2/BayesSPsurv/man/exchangeSPsurv.Rd | 6 BayesSPsurv-0.1.2/BayesSPsurv/man/figures/README-unnamed-chunk-3-1.png |binary BayesSPsurv-0.1.2/BayesSPsurv/man/plot_JoinCount.Rd |only BayesSPsurv-0.1.2/BayesSPsurv/man/plot_Moran.I.Rd | 5 BayesSPsurv-0.1.2/BayesSPsurv/man/pooledSPsurv.Rd | 6 BayesSPsurv-0.1.2/BayesSPsurv/man/spatialSPsurv.Rd | 6 BayesSPsurv-0.1.2/BayesSPsurv/man/spatial_SA.Rd | 2 19 files changed, 209 insertions(+), 100 deletions(-)
Title: Factorization of Sparse Counts Matrices Through Poisson
Likelihood
Description: Creates a low-rank factorization of a sparse counts matrix by maximizing Poisson likelihood with l1/l2 regularization
with all non-negative latent factors (e.g. for recommender systems or topic modeling) (Cortes, (2018) <arXiv:1811.01908>).
Similar to hierarchical Poisson factorization, but follows an optimization-based approach with regularization instead of a
hierarchical structure, and is fit through gradient-based methods instead of variational inference.
Author: David Cortes [aut, cre, cph], Jean-Sebastien Roy [cph], Stephen Nash [cph]
Maintainer: David Cortes <david.cortes.rivera@gmail.com>
Diff between poismf versions 0.2.6 dated 2020-11-13 and 0.2.7 dated 2021-01-08
DESCRIPTION | 10 ++++----- LICENSE | 2 - MD5 | 18 ++++++++--------- NAMESPACE | 5 +++- R/poismf.R | 54 ++++++++++++++++++++++++++------------------------- man/poismf.Rd | 16 ++++++--------- man/poismf_unsafe.Rd | 4 +-- src/poismf.c | 11 ++++------ src/poismf.h | 5 ++-- src/rwrapper.c | 7 ++++-- 10 files changed, 69 insertions(+), 63 deletions(-)
Title: Market Matching and Causal Impact Inference
Description: For a given test market find the best control markets using time series matching and analyze the impact of an intervention. The intervention could be a marketing event or some other local business tactic that is being tested. The workflow implemented in the Market Matching package utilizes dynamic time warping (the 'dtw' package) to do the matching and the 'CausalImpact' package to analyze the causal impact. In fact, this package can be considered a "workflow wrapper" for those two packages. In addition, if you don't have a chosen set of test markets to match, the Market Matching package can provide suggested test/control market pairs and pseudo prospective power analysis (measuring causal impact at fake interventions).
Author: Larsen Kim [aut, cre]
Maintainer: Larsen Kim <kblarsen4@gmail.com>
Diff between MarketMatching versions 1.1.2 dated 2019-07-03 and 1.2.0 dated 2021-01-08
DESCRIPTION | 18 MD5 | 26 - NAMESPACE | 8 R/MarketMatching.R | 79 +++ R/functions.R | 747 +++++++++++++++++++++++++++++++--- README.md | 319 ++++++++++++-- inst/doc/MarketMatching-Vignette.Rmd | 97 ++++ inst/doc/MarketMatching-Vignette.html | 224 ++++++++-- man/MarketMatching.Rd | 77 +++ man/best_matches.Rd | 28 + man/inference.Rd | 2 man/roll_up_optimal_pairs.Rd |only man/test_fake_lift.Rd |only man/weather.Rd | 6 vignettes/MarketMatching-Vignette.Rmd | 97 ++++ 15 files changed, 1528 insertions(+), 200 deletions(-)
More information about MarketMatching at CRAN
Permanent link
Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Michael Curry [aut] (<https://orcid.org/0000-0002-0261-4044>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Joseph Larmarange [ctb] (<https://orcid.org/0000-0001-7097-700X>),
Jessica Lavery [ctb] (<https://orcid.org/0000-0002-2746-5647>),
Stephanie Lobaugh [ctb],
Gustavo Zapata Wainberg [ctb] (<https://orcid.org/0000-0002-2524-3637>)
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.3.5 dated 2020-09-29 and 1.3.6 dated 2021-01-08
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Title: Access Elevation Data from Various APIs
Description: Several web services are available that provide access to elevation
data. This package provides access to several of those services and
returns elevation data either as a SpatialPointsDataFrame from
point elevation services or as a raster object from raster
elevation services. Currently, the package supports access to the
Amazon Web Services Terrain Tiles <https://registry.opendata.aws/terrain-tiles/>,
the Open Topography Global Datasets API <https://opentopography.org/developers/>,
and the USGS Elevation Point Query Service <https://nationalmap.gov/epqs/>.
Author: Jeffrey Hollister [aut, cre] (<https://orcid.org/0000-0002-9254-9740>),
Tarak Shah [ctb],
Alec L. Robitaille [ctb] (<https://orcid.org/0000-0002-4706-1762>),
Marcus W. Beck [rev] (<https://orcid.org/0000-0002-4996-0059>),
Mike Johnson [ctb] (<https://orcid.org/0000-0002-5288-8350>)
Maintainer: Jeffrey Hollister <hollister.jeff@epa.gov>
Diff between elevatr versions 0.3.1 dated 2020-11-23 and 0.3.3 dated 2021-01-08
DESCRIPTION | 6 +- MD5 | 25 +++++------ NAMESPACE | 1 R/get_elev_point.R | 13 +++-- R/get_elev_raster.R | 7 +-- R/internal.R | 77 +++++++++++++++++++++------------- R/zzz.R |only inst/doc/introduction_to_elevatr.html | 4 - man/bbox_to_sp.Rd | 5 +- man/get_elev_point.Rd | 2 man/get_elev_raster.Rd | 4 - tests/testthat/test-get_elev_point.R | 11 ++-- tests/testthat/test-get_elev_raster.R | 13 +++-- tests/testthat/test-internal.R | 21 ++++----- 14 files changed, 110 insertions(+), 79 deletions(-)
Title: Functional Input Validation
Description: A set of basic tools to transform functions into functions with
input validation checks, in a manner suitable for both programmatic and
interactive use.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Diff between valaddin versions 1.0.0 dated 2019-02-10 and 1.0.1 dated 2021-01-08
valaddin-1.0.0/valaddin/NEWS |only valaddin-1.0.1/valaddin/DESCRIPTION | 8 valaddin-1.0.1/valaddin/MD5 | 23 valaddin-1.0.1/valaddin/NEWS.md | 7 valaddin-1.0.1/valaddin/README.md | 65 valaddin-1.0.1/valaddin/build/vignette.rds |binary valaddin-1.0.1/valaddin/inst/doc/valaddin.R | 52 valaddin-1.0.1/valaddin/inst/doc/valaddin.Rmd | 2 valaddin-1.0.1/valaddin/inst/doc/valaddin.html | 1208 +++++++++--------- valaddin-1.0.1/valaddin/man/firmly.Rd | 24 valaddin-1.0.1/valaddin/man/valaddin.Rd | 1 valaddin-1.0.1/valaddin/tests/testthat/test-loosely.R | 7 valaddin-1.0.1/valaddin/vignettes/valaddin.Rmd | 2 13 files changed, 724 insertions(+), 675 deletions(-)
Title: Stratification and Matching for Large Observational Data Sets
Description: A pilot matching design to automatically
stratify and match large datasets. The manual_stratify() function allows
users to manually stratify a dataset based on categorical variables of
interest, while the auto_stratify() function does automatically by
allocating a held-aside (pilot) data set, fitting a prognostic score
(see Hansen (2008) <doi:10.1093/biomet/asn004>) on the pilot set, and stratifying the data set based
on prognostic score quantiles. The strata_match() function then does optimal
matching of the data set in parallel within strata.
Author: Rachael C. Aikens [aut, cre],
Joseph Rigdon [aut],
Justin Lee [aut],
Michael Baiocchi [aut],
Jonathan Chen [aut]
Maintainer: Rachael C. Aikens <rockyaikens@gmail.com>
Diff between stratamatch versions 0.1.5 dated 2020-04-09 and 0.1.6 dated 2021-01-08
stratamatch-0.1.5/stratamatch/man/make_fm_plot.Rd |only stratamatch-0.1.6/stratamatch/DESCRIPTION | 12 stratamatch-0.1.6/stratamatch/MD5 | 86 - stratamatch-0.1.6/stratamatch/NAMESPACE | 4 stratamatch-0.1.6/stratamatch/R/ICU_data_documentation.R | 4 stratamatch-0.1.6/stratamatch/R/S3_methods.R | 404 +++--- stratamatch-0.1.6/stratamatch/R/auto_stratify.R | 346 +++-- stratamatch-0.1.6/stratamatch/R/imported_functions.R | 2 stratamatch-0.1.6/stratamatch/R/make_issue_table.R | 33 stratamatch-0.1.6/stratamatch/R/make_sample_data.R | 46 stratamatch-0.1.6/stratamatch/R/manual_stratify.R | 75 - stratamatch-0.1.6/stratamatch/R/match_functions.R | 74 - stratamatch-0.1.6/stratamatch/R/split_pilot_set.R | 170 +- stratamatch-0.1.6/stratamatch/R/strata_object_constructors.R | 65 stratamatch-0.1.6/stratamatch/R/stratamatch.R | 2 stratamatch-0.1.6/stratamatch/inst/doc/Intro_to_stratamatch.R | 60 stratamatch-0.1.6/stratamatch/inst/doc/Intro_to_stratamatch.Rmd | 42 stratamatch-0.1.6/stratamatch/inst/doc/Intro_to_stratamatch.html | 159 +- stratamatch-0.1.6/stratamatch/man/ICU_data.Rd | 6 stratamatch-0.1.6/stratamatch/man/auto_stratify.Rd | 79 - stratamatch-0.1.6/stratamatch/man/build_autostrata.Rd | 21 stratamatch-0.1.6/stratamatch/man/check_base_inputs_auto_stratify.Rd | 2 stratamatch-0.1.6/stratamatch/man/check_pilot_set_options.Rd | 20 stratamatch-0.1.6/stratamatch/man/check_scores.Rd | 6 stratamatch-0.1.6/stratamatch/man/extract_cut_points.Rd |only stratamatch-0.1.6/stratamatch/man/extract_cut_points.auto_strata.Rd |only stratamatch-0.1.6/stratamatch/man/is.auto_strata.Rd | 4 stratamatch-0.1.6/stratamatch/man/is.manual_strata.Rd | 4 stratamatch-0.1.6/stratamatch/man/is.strata.Rd | 4 stratamatch-0.1.6/stratamatch/man/make_ac_plot.Rd |only stratamatch-0.1.6/stratamatch/man/make_hist_plot.Rd | 11 stratamatch-0.1.6/stratamatch/man/make_resid_plot.Rd | 4 stratamatch-0.1.6/stratamatch/man/make_sample_data.Rd | 4 stratamatch-0.1.6/stratamatch/man/manual_stratify.Rd | 16 stratamatch-0.1.6/stratamatch/man/new_auto_strata.Rd | 14 stratamatch-0.1.6/stratamatch/man/new_manual_strata.Rd | 11 stratamatch-0.1.6/stratamatch/man/plot.strata.Rd | 44 stratamatch-0.1.6/stratamatch/man/split_pilot_set.Rd | 34 stratamatch-0.1.6/stratamatch/man/strata_match.Rd | 4 stratamatch-0.1.6/stratamatch/man/stratamatch.Rd | 1 stratamatch-0.1.6/stratamatch/tests/testthat/test-S3_functions.R | 128 + stratamatch-0.1.6/stratamatch/tests/testthat/test-auto_stratify.R | 668 ++++++---- stratamatch-0.1.6/stratamatch/tests/testthat/test-manual_stratify.R | 200 +- stratamatch-0.1.6/stratamatch/tests/testthat/test-match_functions.R | 32 stratamatch-0.1.6/stratamatch/tests/testthat/test-split_pilot_set.R | 192 ++ stratamatch-0.1.6/stratamatch/vignettes/Intro_to_stratamatch.Rmd | 42 46 files changed, 1912 insertions(+), 1223 deletions(-)
Title: Automates the Creation of New Statistical Analysis Projects
Description: Provides functions to
automatically build a directory structure for a new R
project. Using this structure, 'ProjectTemplate'
automates data loading, preprocessing, library
importing and unit testing.
Author: Aleksandar Blagotic [ctb],
Diego Valle-Jones [ctb],
Jeffrey Breen [ctb],
Joakim Lundborg [ctb],
John Myles White [aut, cph],
Josh Bode [ctb],
Kenton White [ctb, cre],
Kirill Mueller [ctb],
Matteo Redaelli [ctb],
Noah Lorang [ctb],
Patrick Schalk [ctb],
Dominik Schneider [ctb],
Gerold Hepp [ctb]
Maintainer: Kenton White <jkentonwhite@gmail.com>
Diff between ProjectTemplate versions 0.9.3 dated 2020-12-04 and 0.10.0 dated 2021-01-08
DESCRIPTION | 49 ++++--- MD5 | 39 +++--- NEWS.md | 10 + R/cache.R | 135 +++++++++++++++++----- R/clear.cache.R | 51 ++++---- R/load.project.R | 6 R/project.config.R | 9 + build/partial.rdb |binary inst/defaults/config/default.dcf | 3 inst/defaults/config/types.dcf | 1 inst/defaults/templates/full/config/global.dcf | 5 inst/defaults/templates/minimal/config/global.dcf | 5 man/cache.Rd | 10 + man/internal.cache.filename.Rd | 6 man/internal.cache.format.Rd |only man/project.config.Rd | 9 + tests/testthat/helper-functions.R |only tests/testthat/test-cache.R | 6 tests/testthat/test-clear.R | 6 tests/testthat/test-load.R | 10 - tests/testthat/test-migration.R | 11 - tests/testthat/test-qs.R |only 22 files changed, 243 insertions(+), 128 deletions(-)
More information about ProjectTemplate at CRAN
Permanent link
Title: Profiling Inference Functions for Various Model Classes
Description: Provides tools that can be used to calculate, evaluate, plot and use for inference the profiles of *arbitrary* inference functions for *arbitrary* 'glm'-like fitted models with linear predictors. More information on the methods that are implemented can be found in Kosmidis (2008) <https://www.r-project.org/doc/Rnews/Rnews_2008-2.pdf>.
Author: Ioannis Kosmidis [aut, cre] (<https://orcid.org/0000-0003-1556-0302>)
Maintainer: Ioannis Kosmidis <ioannis.kosmidis@warwick.ac.uk>
Diff between profileModel versions 0.6.0 dated 2019-04-03 and 0.6.1 dated 2021-01-08
DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- R/profileModel.R | 4 ++-- inst/CHANGES | 13 ++++++++++++- man/confintModel.Rd | 4 ++-- man/objectives.Rd | 2 +- man/plot.profileModel.Rd | 4 ++-- man/print.profileModel.Rd | 4 ++-- man/profileModel.Rd | 4 ++-- man/signedSquareRoots.Rd | 4 ++-- 10 files changed, 38 insertions(+), 27 deletions(-)
Title: Low-Cost Anonymous Functions
Description: Provides a compact variation of the usual syntax of function
declaration, in order to support tidyverse-style quasiquotation of a
function's arguments and body.
Author: Eugene Ha [aut, cre]
Maintainer: Eugene Ha <eha@posteo.de>
Diff between nofrills versions 0.3.0 dated 2018-01-21 and 0.3.1 dated 2021-01-08
DESCRIPTION | 14 ++++----- LICENSE | 2 - MD5 | 23 +++++++------- NEWS | 9 +++++ R/closure.R |only R/curry.R | 2 - R/fn.R | 15 +++------ README.md | 57 +++++++++++++++++-------------------- man/curry.Rd | 12 +++---- man/fn.Rd | 23 ++++++-------- man/make_fn_aware.Rd | 2 - man/nofrills-package.Rd | 4 +- tests/testthat/test-abbreviation.R | 18 +++++++---- 13 files changed, 93 insertions(+), 88 deletions(-)
Title: Maximum Likelihood Analysis of Animal Movement Behavior Using
Multivariate Hidden Markov Models
Description: Extended tools for analyzing telemetry data using generalized hidden Markov models. Features of momentuHMM (pronounced ``momentum'') include data pre-processing and visualization, fitting HMMs to location and auxiliary biotelemetry or environmental data, biased and correlated random walk movement models, hierarchical HMMs, multiple imputation for incorporating location measurement error and missing data, user-specified design matrices and constraints for covariate modelling of parameters, random effects, decoding of the state process, visualization of fitted models, model checking and selection, and simulation. See McClintock and Michelot (2018) <doi:10.1111/2041-210X.12995>.
Author: Brett McClintock, Theo Michelot
Maintainer: Brett McClintock <brett.mcclintock@noaa.gov>
Diff between momentuHMM versions 1.5.1 dated 2020-03-06 and 1.5.2 dated 2021-01-08
DESCRIPTION | 21 - MD5 | 178 ++++----- NAMESPACE | 35 - NEWS | 39 ++ R/AIC_momentuHMM.R | 18 R/AICweights.R | 1 R/CIbeta.R | 22 - R/CIreal.R | 34 - R/MIfitHMM.R | 84 ++-- R/MIpool.R | 44 -- R/allProbs.R | 10 R/checkInputs.R | 8 R/checkPar0.R | 28 - R/crawlWrap.R | 500 +++++++++++++------------- R/distAngle.R | 2 R/exampleData.R | 6 R/fitHMM.R | 87 +--- R/formatHierFormula.R | 10 R/formatHierHMM.R | 52 +- R/formatRecharge.R | 18 R/formatmiSum.R | 6 R/getCovNames.R | 8 R/getDM.R | 90 +--- R/getPar.R | 14 R/getPar0.R | 31 - R/getParDM.R | 74 +-- R/getSplineDM.R | 20 - R/getTrProbs.R | 8 R/getXB.R | 13 R/get_fixParIndex.R | 10 R/mixtureProbs.R | 32 - R/momentuHMM_utils.R | 21 - R/moveHMMwrap.R | 6 R/n2w.R | 26 - R/nLogLike.R | 16 R/plotPR.R | 10 R/plotSat.R | 43 +- R/plotSpatialCov.R | 74 ++- R/plotStationary.R | 10 R/plot_crwData.R | 10 R/plot_miHMM.R | 4 R/plot_miSum.R | 4 R/plot_momentuHMM.R | 44 +- R/prepData.R | 24 - R/print_miHMM.R | 2 R/print_miSum.R | 2 R/print_momentuHMM.R | 19 R/pseudoRes.R | 10 R/randomEffects.R |only R/simData.R | 179 ++++----- R/simHierData.R | 171 +++++--- R/simObsData.R | 6 R/stateFormulas.R | 62 +-- R/stateProbs.R | 2 R/stationary.R | 6 R/timeInStates.R | 35 + R/viterbi.R | 43 -- R/w2n.R | 41 +- README.md | 2 build/vignette.rds |binary data/example.rda |binary data/miExample.rda |binary inst/doc/momentuHMM.pdf |binary man/MIfitHMM.Rd | 21 - man/MIpool.Rd | 2 man/checkPar0.Rd | 8 man/crawlWrap.Rd | 2 man/exampleData.Rd | 6 man/fitHMM.Rd | 22 - man/getParDM.Rd | 13 man/n2w.Rd | 26 - man/nLogLike.Rd | 14 man/plot.miHMM.Rd | 4 man/plot.miSum.Rd | 4 man/plot.momentuHMM.Rd | 2 man/plotPR.Rd | 2 man/plotSat.Rd | 8 man/plotSpatialCov.Rd | 11 man/plotStationary.Rd | 2 man/prepData.Rd | 4 man/print.miHMM.Rd | 2 man/print.miSum.Rd | 2 man/randomEffects.Rd |only man/simData.Rd | 26 - man/w2n.Rd | 14 src/densities.h | 2 vignettes/examples/codExample.R | 2 vignettes/examples/greySealExample.R | 2 vignettes/examples/hornSharkExample.R | 14 vignettes/examples/pilotWhaleExample.R | 2 vignettes/examples/turtleExample_rw_mvnorm2.R | 2 91 files changed, 1301 insertions(+), 1293 deletions(-)
Title: Collect ESPN Fantasy Football Data
Description: Format the raw data from the ESPN fantasy football
API <https://fantasy.espn.com/apis/v3/games/ffl/> into tidy tables.
Scrape data on public leagues, rosters, athletes, and matches.
Author: Kiernan Nicholls [aut, cre]
Maintainer: Kiernan Nicholls <kiernann@protonmail.com>
Diff between fflr versions 0.3.13 dated 2020-11-25 and 0.3.15 dated 2021-01-08
DESCRIPTION | 6 MD5 | 22 +- NEWS.md | 7 R/roster-moves.R | 2 build/vignette.rds |binary inst/doc/fantasy-football.R | 2 inst/doc/fantasy-football.Rmd | 2 inst/doc/fantasy-football.html | 328 +++++++++++++++++------------------------ man/roster_moves.Rd | 2 tests/testthat/test-correct.R | 3 tests/testthat/test-live.R | 9 - vignettes/fantasy-football.Rmd | 2 12 files changed, 177 insertions(+), 208 deletions(-)
Title: Quantitative Analysis Made Accessible
Description: This is a new version of the 'userfriendlyscience' package,
which has grown a bit unwieldy. Therefore, distinct functionalities
are being 'consciously uncoupled' into different packages. This package
contains the general-purpose tools and utilities (see the
'behaviorchange' package, the 'rosetta' package, and the
soon-to-be-released 'scd' package for other functionality), and
is the most direct 'successor' of the original 'userfriendlyscience' package.
For example, this package contains a number of basic functions to create
higher level plots, such as diamond plots, to easily plot sampling
distributions, to generate confidence intervals, to plan study sample sizes
for confidence intervals, and to do some basic operations such as
(dis)attenuate effect size estimates.
Author: Gjalt-Jorn Peters [aut, cre] (<https://orcid.org/0000-0002-0336-9589>),
Stefan Gruijters [ctb] (<https://orcid.org/0000-0003-0141-0071>)
Maintainer: Gjalt-Jorn Peters <gjalt-jorn@userfriendlyscience.com>
Diff between ufs versions 0.4.0 dated 2020-11-10 and 0.4.1 dated 2021-01-08
DESCRIPTION | 6 - MD5 | 82 +++++++++--------- NAMESPACE | 3 R/CIM.R | 167 ++++++++++++++++++++++---------------- R/associationsDiamondPlot.R | 4 R/attenuate.d.R | 2 R/biAxisDiamondPlot.R | 4 R/convert.d.to.nnc.R | 2 R/descr.R | 34 +++++++ R/diamondPlot.R | 4 R/disattenuate.d.R | 2 R/duoComparisonDiamondPlot.R | 4 R/escapeRegex_(from_Hmisc).R | 2 R/factorLoadingDiamondCIplot.R | 6 - R/factorLoadingHeatmap.R |only R/ggSave.R | 4 R/kblXtra.R | 48 +++++++--- R/meanSDtoDiamondPlot.R | 4 R/meansComparisonDiamondPlot.R | 4 R/meansDiamondPlot.R | 4 R/modus.R | 2 R/opts.R | 7 + R/regrInfluential.R | 37 ++++---- R/scaleStructure.R | 16 +-- R/vecTxt.R | 16 +++ README.md | 11 ++ build/partial.rdb |binary man/associationsDiamondPlot.Rd | 2 man/attenuate.d.Rd | 2 man/biAxisDiamondPlot.Rd | 2 man/comparisonDiamondPlots.Rd | 4 man/descriptives.Rd | 2 man/diamondPlot.Rd | 2 man/disattenuate.d.Rd | 2 man/escapeRegex.Rd | 2 man/factorLoadingDiamondCIplot.Rd | 4 man/factorLoadingHeatmap.Rd |only man/kblXtra.Rd | 11 ++ man/meanSDtoDiamondPlot.Rd | 2 man/meansDiamondPlot.Rd | 2 man/nncConversion.Rd | 2 man/scaleStructure.Rd | 16 +-- man/vecTxt.Rd | 10 ++ 43 files changed, 332 insertions(+), 208 deletions(-)
Title: A Grammar of Clinical Data Summary
Description: A tool created to simplify the data manipulation necessary to create clinical reports.
Author: Eli Miller [aut] (<https://orcid.org/0000-0002-2127-9456>),
Mike Stackhouse [aut, cre] (<https://orcid.org/0000-0001-6030-723X>),
Ashley Tarasiewicz [aut],
Nathan Kosiba [aut] (<https://orcid.org/0000-0001-5359-4234>),
Atorus Research LLC [cph]
Maintainer: Mike Stackhouse <mike.stackhouse@atorusresearch.com>
Diff between Tplyr versions 0.2.2 dated 2020-11-30 and 0.3.1 dated 2021-01-08
DESCRIPTION | 6 MD5 | 82 ++++----- NAMESPACE | 1 NEWS.md | 21 ++ R/count.R | 61 +++++-- R/count_bindings.R | 12 - R/format.R | 127 +++++++++------ R/prebuild.R | 36 +++- R/print.R | 2 R/sort.R | 35 ++-- R/table_bindings.R | 44 +++-- R/utils.R | 3 R/zzz.R | 4 README.md | 12 - build/vignette.rds |binary inst/doc/Tplyr.Rmd | 8 inst/doc/Tplyr.html | 215 ++++++++++++++++++++++++- inst/doc/count.R | 2 inst/doc/count.Rmd | 4 inst/doc/count.html | 107 ++++++++++++ inst/doc/denom.R | 4 inst/doc/denom.Rmd | 4 inst/doc/denom.html | 327 +++++++++++++++++++++++++++++---------- inst/doc/desc.html | 163 +++++++++++++++++-- inst/doc/options.html | 127 ++++++++++++++- inst/doc/shift.html | 97 +++++++++++ inst/doc/table.Rmd | 2 inst/doc/table.html | 127 ++++++++++++++- man/apply_row_masks.Rd | 2 man/header_n.Rd | 32 ++- man/ordering.Rd | 12 - tests/testthat/fstr_print.txt | 2 tests/testthat/fstr_str.txt | 2 tests/testthat/layer_str.txt | 1 tests/testthat/test-count.R | 61 ++++++- tests/testthat/test-functional.R | 31 +++ tests/testthat/test-print.R | 2 tests/testthat/test-sort.R | 34 ++++ vignettes/Tplyr.Rmd | 8 vignettes/count.Rmd | 4 vignettes/denom.Rmd | 4 vignettes/table.Rmd | 2 42 files changed, 1511 insertions(+), 319 deletions(-)
Title: Calculate Task Split Half Reliability Estimates
Description: Estimate the internal consistency of your tasks with a permutation based split-half reliability approach.
Unofficial release name: "Kitten Mittens".
Author: Sam Parsons [aut, cre]
Maintainer: Sam Parsons <sam.parsons@psy.ox.ac.uk>
Diff between splithalf versions 0.7.1 dated 2020-03-18 and 0.7.2 dated 2021-01-08
DESCRIPTION | 12 MD5 | 27 + NAMESPACE | 68 ++-- NEWS.md | 133 +++++--- R/data.R |only R/splithalf_multiverse.R | 78 +++-- R/zzz.R | 5 README.md | 647 ++++++++++++++++++++++++++++++++++++++++++- data |only inst/hexlogo |only man/figures |only man/multiverse.plot.Rd | 90 ++--- man/speedtestdata.Rd |only man/splithalf.Rd | 154 +++++----- man/splithalf.multiverse.Rd | 44 +- man/testretest.multiverse.Rd | 74 ++-- 16 files changed, 1013 insertions(+), 319 deletions(-)
Title: Compositional Data Analysis
Description: Provides functions for the consistent analysis of compositional
data (e.g. portions of substances) and positive numbers (e.g. concentrations)
in the way proposed by J. Aitchison and V. Pawlowsky-Glahn.
Author: K. Gerald van den Boogaart <boogaart@hzdr.de>,
Raimon Tolosana-Delgado, Matevz Bren
Maintainer: K. Gerald van den Boogaart <support@boogaart.de>
Diff between compositions versions 2.0-0 dated 2020-07-14 and 2.0-1 dated 2021-01-08
DESCRIPTION | 12 MD5 | 102 ++-- R/Geostat.R | 2 R/and.R | 33 - R/compositions.R | 36 - build/partial.rdb |binary build/vignette.rds |binary inst/doc/UsingCompositions.pdf |binary inst/doc/UsingCompositions.rnw | 4 inst/doc/compositions_v2.html | 883 +++++++++++++++++++++------------------- man/Aar.Rd | 4 man/Hydrochem.Rd | 2 man/SimulatedAmounts.Rd | 2 man/acomp.Rd | 6 man/acomparith.Rd | 4 man/acompmargin.Rd | 2 man/alr.Rd | 2 man/aplus.Rd | 2 man/apt.Rd | 2 man/arrows3d.Rd | 8 man/axis3d.Rd | 8 man/backtransform.Rd | 2 man/balancebase.Rd | 4 man/biplot3d.Rd | 8 man/cdt.Rd | 2 man/codadendrogram.Rd | 2 man/compositions.Rd | 8 man/cpt.Rd | 2 man/gsigetbalstruct.Rd | 2 man/gsimerge2signary.Rd | 2 man/gsivarwithlosts.Rd | 2 man/idt.Rd | 2 man/iit.Rd | 2 man/ilr.Rd | 2 man/ilrBase.Rd | 2 man/ilt.Rd | 2 man/ipt.Rd | 2 man/pairwisePlot.Rd | 6 man/plot.Rd | 4 man/plot3d.Rd | 6 man/plot3dacomp.Rd | 10 man/plot3daplus.Rd | 5 man/plot3drmult.Rd | 6 man/plot3drplus.Rd | 6 man/princompacomp.Rd | 7 man/pwlr.Rd | 2 man/pwlrPlot.Rd | 6 man/rDirichlet.Rd | 2 man/rcomp.Rd | 2 man/rplus.Rd | 2 man/zeroreplace.Rd | 4 vignettes/UsingCompositions.rnw | 4 52 files changed, 654 insertions(+), 578 deletions(-)
Title: A Graphical Tool for Wavelet (Cross) Correlation and Wavelet
Multiple (Cross) Correlation Analysis
Description: Set of functions that improves the graphical presentations of the functions: wave.correlation and spin.correlation (waveslim package, Whitcher 2012) and the wave.multiple.correlation and wave.multiple.cross.correlation (wavemulcor package, Fernandez-Macho 2012b). The plot outputs (heatmaps) can be displayed in the screen or can be saved as PNG or JPG images or as PDF or EPS formats. The W2CWM2C package also helps to handle the (input data) multivariate time series easily as a list of N elements (times series) and provides a multivariate data set (dataexample) to exemplify its use. A description of the package was published in a scientific paper: Polanco-Martinez and Fernandez-Macho (2014), <doi:10.1109/MCSE.2014.96>.
Author: Josue M. Polanco-Martinez [aut, cre]
(<https://orcid.org/0000-0001-7164-0185>)
Maintainer: Josue M. Polanco-Martinez <josue.m.polanco@gmail.com>
Diff between W2CWM2C versions 2.0 dated 2015-08-05 and 2.2 dated 2021-01-08
DESCRIPTION | 18 +++++++----- MD5 | 23 ++++++++-------- R/WC.R | 27 ++++++++++++++++++- R/WCC.R | 23 ++++++++++++++++ R/WMC.R | 23 ++++++++++++++++ R/WMCC.R | 23 ++++++++++++++++ build |only man/W2CWM2C-package.Rd | 68 ++++++++++++++++++++++++++----------------------- man/WC.Rd | 36 ++++++++++++------------- man/WCC.Rd | 41 ++++++++++++++++------------- man/WMC.Rd | 38 ++++++++++++++------------- man/WMCC.Rd | 34 +++++++++++------------- man/dataexample.Rd | 2 - 13 files changed, 231 insertions(+), 125 deletions(-)
Title: 'SQLite' Interface for R
Description: Embeds the 'SQLite' database engine in R and
provides an interface compliant with the 'DBI' package. The source for
the 'SQLite' engine is included.
Author: Kirill Müller [aut, cre] (<https://orcid.org/0000-0002-1416-3412>),
Hadley Wickham [aut],
David A. James [aut],
Seth Falcon [aut],
SQLite Authors [ctb] (for the included SQLite sources),
Liam Healy [ctb] (for the included SQLite sources),
R Consortium [fnd],
RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>
Diff between RSQLite versions 2.2.1 dated 2020-09-30 and 2.2.2 dated 2021-01-08
DESCRIPTION | 11 MD5 | 28 NEWS.md | 17 R/extensions.R | 8 R/regularExpressions.R | 3 R/table.R | 21 R/transactions.R | 5 README.md | 82 - build/vignette.rds |binary inst/doc/RSQLite.html | 172 +- src/SqliteResultImpl.cpp | 2 src/vendor/sqlite3/sqlite3.c | 2683 +++++++++++++++++++++++++++---------- src/vendor/sqlite3/sqlite3.h | 79 - src/vendor/sqlite3/sqlite3ext.h | 4 tests/testthat/test-dbWriteTable.R | 6 15 files changed, 2217 insertions(+), 904 deletions(-)
Title: Factor Big Integers with the Parallel Quadratic Sieve
Description: Features the multiple polynomial quadratic sieve (MPQS) algorithm
for factoring large integers and a vectorized factoring function that
returns the complete factorization of an integer. The MPQS is based off of
the seminal work of Carl Pomerance (1984) <doi:10.1007/3-540-39757-4_17>
along with the modification of multiple polynomials introduced by Peter
Montgomery and J. Davis as outlined by Robert D. Silverman (1987)
<doi:10.1090/S0025-5718-1987-0866119-8>. Utilizes the C library
GMP (GNU Multiple Precision Arithmetic) and 'RcppThread' for factoring
integers in parallel. For smaller integers, a simple Elliptic
Curve algorithm is attempted followed by a constrained version of
Pollard's rho algorithm. The Pollard's rho algorithm is the same algorithm
used by the factorize function in the 'gmp' package.
Author: Joseph Wood [aut, cre],
Free Software Foundation, Inc. [cph],
Mike Tryczak [ctb]
Maintainer: Joseph Wood <jwood000@gmail.com>
Diff between RcppBigIntAlgos versions 1.0.0 dated 2020-12-12 and 1.0.1 dated 2021-01-08
DESCRIPTION | 6 ++--- MD5 | 10 ++++----- NEWS | 4 +++ README.md | 46 +++++++++++++++++++++++++++++++++-------- inst/include/LenstraECM.h | 9 ++++---- src/PrimeFactorUtils.cpp | 51 +++++++++++++++++++++++++++------------------- 6 files changed, 85 insertions(+), 41 deletions(-)
More information about RcppBigIntAlgos at CRAN
Permanent link
Title: Rapid Realistic Routing with 'R5'
Description: Rapid realistic routing on multimodal transport networks (walk,
bike, public transport and car) using 'R5', the Rapid Realistic
Routing on Real-world and Reimagined networks
<https://github.com/conveyal/r5>. The package allows users to
generate detailed routing analysis or calculate travel time matrices
using seamless parallel computing on top of the R5 Java machine.
Author: Marcus Saraiva [aut] (<https://orcid.org/0000-0001-6218-2338>),
Rafael H. M. Pereira [aut, cre]
(<https://orcid.org/0000-0003-2125-7465>),
Daniel Herszenhut [aut] (<https://orcid.org/0000-0001-8066-1105>),
Carlos Kaue Vieira Braga [aut]
(<https://orcid.org/0000-0002-6104-7297>),
Matthew Wigginton Conway [ctb],
Ipea - Institue for Applied Economic Research [cph, fnd]
Maintainer: Rafael H. M. Pereira <rafa.pereira.br@gmail.com>
Diff between r5r versions 0.3-1 dated 2021-01-07 and 0.3-2 dated 2021-01-08
DESCRIPTION | 8 ++++---- MD5 | 8 ++++---- NEWS.md | 6 +++++- R/utils.R | 5 ++--- inst/doc/intro_to_r5r.html | 16 ++++++++-------- 5 files changed, 23 insertions(+), 20 deletions(-)
Title: Implementation of 2D Correlation Analysis in R
Description: Implementation of two-dimensional (2D) correlation analysis based
on the Fourier-transformation approach described by Isao Noda (I. Noda
(1993) <DOI:10.1366/0003702934067694>). Additionally there are two plot
functions for the resulting correlation matrix: The first one creates
colored 2D plots, while the second one generates 3D plots.
Author: Robert Geitner [cre, aut],
Robby Fritzsch [aut],
Thomas Bocklitz [aut],
Juergen Popp [ctb, cph]
Maintainer: Robert Geitner <robert.geitner@uni-jena.de>
Diff between corr2D versions 1.0.0 dated 2019-07-29 and 1.0.2 dated 2021-01-08
DESCRIPTION | 23 +++++++++++------------ MD5 | 18 ++++++++++-------- NEWS.md |only README.md |only build/vignette.rds |binary man/FuranMale.Rd | 4 +++- man/codis2d.Rd | 16 ++++++++++++---- man/corr2d.Rd | 19 +++++++++++++++---- man/plot_corr2d.Rd | 36 ++++++++++++++++++++++++++++-------- man/plot_corr2din3d.Rd | 17 +++++++++++++---- man/sim2ddata.Rd | 16 +++++++++++++--- 11 files changed, 105 insertions(+), 44 deletions(-)
Title: Fitting the copCAR Regression Model for Discrete Areal Data
Description: Provides tools for fitting the copCAR (Hughes, 2015)
<DOI:10.1080/10618600.2014.948178> regression model for discrete
areal data. Three types of estimation are supported (continuous
extension, composite marginal likelihood, and distributional transform),
for three types of outcomes (Bernoulli, negative binomial, and Poisson).
Author: Emily Goren <emily.goren@gmail.com> and John Hughes
<drjphughesjr@gmail.com>
Maintainer: John Hughes <drjphughesjr@gmail.com>
Diff between copCAR versions 2.0-3 dated 2020-05-08 and 2.0-4 dated 2021-01-08
DESCRIPTION | 8 - MD5 | 6 R/copCAR.R | 361 ++++++++++++++++++++++++++++++------------------------------ R/zzz.R | 2 4 files changed, 190 insertions(+), 187 deletions(-)
Title: Aligned Corpus Toolkit
Description: The Aligned Corpus Toolkit (act) is designed for linguists that work with time aligned transcription data. It offers functions to import and export various annotation file formats ('ELAN' .eaf, 'EXMARaLDA .exb and 'Praat' .TextGrid files), create print transcripts in the style of conversation analysis, search transcripts (span searches across multiple annotations, search in normalized annotations, make concordances etc.), export and re-import search results (.csv and 'Excel' .xlsx format), create cuts for the search results (print transcripts, audio/video cuts using 'FFmpeg' and video sub titles in 'Subrib title' .srt format), modify the data in a corpus (search/replace, delete, filter etc.), interact with 'Praat' using 'Praat'-scripts, and exchange data with the 'rPraat' package. The package is itself written in R and may be expanded by other users.
Author: Oliver Ehmer [aut, cre]
Maintainer: Oliver Ehmer <oliver.ehmer@romanistik.uni-freiburg.de>
Diff between act versions 0.94 dated 2020-11-04 and 1.0 dated 2021-01-08
act-0.94/act/LICENSE |only act-0.94/act/R/corpus__________________________.R |only act-0.94/act/R/corpus__class.R |only act-0.94/act/R/corpus_load.R |only act-0.94/act/R/io________________________________.R |only act-0.94/act/R/io_eaf_export.R |only act-0.94/act/R/io_export.R |only act-0.94/act/R/io_textgrid_export.R |only act-0.94/act/R/io_textgrid_import.R |only act-0.94/act/R/media____________________________.R |only act-0.94/act/R/media_getpath.R |only act-0.94/act/R/media_remove.R |only act-0.94/act/R/modify____________________________.R |only act-0.94/act/R/modify_data_delete.R |only act-0.94/act/R/modify_data_delete_empty.R |only act-0.94/act/R/modify_data_matrix.R |only act-0.94/act/R/modify_data_replace_copy.R |only act-0.94/act/R/modify_tiers_rename.R |only act-0.94/act/R/modify_tiers_reorder.R |only act-0.94/act/R/modify_transcripts_merge.R |only act-0.94/act/R/praat.R |only act-0.94/act/R/praat______________________________.R |only act-0.94/act/R/search____________________________.R |only act-0.94/act/R/search__class.R |only act-0.94/act/R/search_fulltext_update.R |only act-0.94/act/R/search_normalize.R |only act-0.94/act/R/snippets____________________________.R |only act-0.94/act/R/snippets_cutlist.R |only act-0.94/act/R/snippets_printtranscript.R |only act-0.94/act/R/snippets_printtranscripts_for_search.R |only act-0.94/act/R/transcript___________________________.R |only act-0.94/act/R/transcript__class.R |only act-0.94/act/inst/examples/corpus_load.R |only act-0.94/act/inst/examples/io_eaf_export.R |only act-0.94/act/inst/examples/io_textgrid_export.R |only act-0.94/act/inst/examples/io_textgrid_import.R |only act-0.94/act/inst/examples/io_transcripts_export.R |only act-0.94/act/inst/examples/media_getpath.R |only act-0.94/act/inst/examples/modify_data_delete.R |only act-0.94/act/inst/examples/modify_data_delete_empty.R |only act-0.94/act/inst/examples/modify_data_matrix.R |only act-0.94/act/inst/examples/modify_data_replace_copy.R |only act-0.94/act/inst/examples/modify_tiers_rename.R |only act-0.94/act/inst/examples/modify_tiers_reorder.R |only act-0.94/act/inst/examples/modify_transcripts_merge.R |only act-0.94/act/inst/examples/snippets_cutlist.R |only act-0.94/act/inst/examples/snippets_printtranscript.R |only act-0.94/act/inst/examples/snippets_printtranscripts_for_search.R |only act-0.94/act/inst/extdata/examplecorpus/sync/SYNC_rotar_y_flexionar.TextGrid |only act-0.94/act/man/corpus_alldata.Rd |only act-0.94/act/man/corpus_load.Rd |only act-0.94/act/man/corpus_overview.Rd |only act-0.94/act/man/eaf_export.Rd |only act-0.94/act/man/fulltext_update.Rd |only act-0.94/act/man/media_getpath.Rd |only act-0.94/act/man/media_remove.Rd |only act-0.94/act/man/modify_data_delete.Rd |only act-0.94/act/man/modify_data_delete_empty.Rd |only act-0.94/act/man/modify_data_matrix.Rd |only act-0.94/act/man/modify_data_replace_copy.Rd |only act-0.94/act/man/modify_tiers_rename.Rd |only act-0.94/act/man/modify_tiers_reorder.Rd |only act-0.94/act/man/modify_transcripts_merge.Rd |only act-0.94/act/man/normalize.Rd |only act-0.94/act/man/options_remove.Rd |only act-0.94/act/man/praat_open_result.Rd |only act-0.94/act/man/praat_search_and_open.Rd |only act-0.94/act/man/snippets_cutlist.Rd |only act-0.94/act/man/snippets_printtranscript.Rd |only act-0.94/act/man/snippets_printtranscripts_search.Rd |only act-0.94/act/man/textgrid_export.Rd |only act-0.94/act/man/textgrid_import.Rd |only act-0.94/act/man/transcripts_export.Rd |only act-1.0/act/DESCRIPTION | 16 act-1.0/act/MD5 | 332 ++++++---- act-1.0/act/NAMESPACE | 81 +- act-1.0/act/R/act-package.R | 73 -- act-1.0/act/R/act_info.R |only act-1.0/act/R/act_info_summarized.R |only act-1.0/act/R/act_options.R | 218 ++++-- act-1.0/act/R/annotations_____________________.R |only act-1.0/act/R/annotations_delete.R |only act-1.0/act/R/annotations_delete_empty.R |only act-1.0/act/R/annotations_matrix.R |only act-1.0/act/R/annotations_replace_copy.R |only act-1.0/act/R/anotations_all.R |only act-1.0/act/R/class__________________________.R |only act-1.0/act/R/class_corpus.R |only act-1.0/act/R/class_layout.R |only act-1.0/act/R/class_search.R |only act-1.0/act/R/class_transcript.R |only act-1.0/act/R/corpus_________________________.R |only act-1.0/act/R/corpus_examplecorpus.R | 2 act-1.0/act/R/corpus_export.R |only act-1.0/act/R/corpus_import.R |only act-1.0/act/R/corpus_new.R | 119 +++ act-1.0/act/R/export_eaf.R |only act-1.0/act/R/export_exb.R |only act-1.0/act/R/export_printtranscript.R |only act-1.0/act/R/export_rpraat.R |only act-1.0/act/R/export_srt.R |only act-1.0/act/R/export_textgrid.R |only act-1.0/act/R/helper__________________________.R |only act-1.0/act/R/helper_format_time.R |only act-1.0/act/R/helper_no_export.R | 115 +-- act-1.0/act/R/helper_tiers_merge_tables.R |only act-1.0/act/R/helper_tiers_new_table.R |only act-1.0/act/R/helper_tiers_sort_table.R |only act-1.0/act/R/helper_transcriptNames_get.R |only act-1.0/act/R/helper_transcriptNames_make.R |only act-1.0/act/R/helper_transcriptNames_set.R |only act-1.0/act/R/import.R |only act-1.0/act/R/import_eaf.R |only act-1.0/act/R/import_exb.R |only act-1.0/act/R/import_rpraat.R |only act-1.0/act/R/import_textgrid.R |only act-1.0/act/R/matrix__________________________.R |only act-1.0/act/R/matrix_load.R | 26 act-1.0/act/R/matrix_save.R | 12 act-1.0/act/R/media__________________________.R |only act-1.0/act/R/media_assign.R | 173 +++-- act-1.0/act/R/media_delete.R |only act-1.0/act/R/media_getPathToExistingFile.R |only act-1.0/act/R/search__________________________.R |only act-1.0/act/R/search_concordance.R | 57 - act-1.0/act/R/search_cuts_media.R |only act-1.0/act/R/search_cuts_printtranscript.R |only act-1.0/act/R/search_cuts_srt.R |only act-1.0/act/R/search_import_export.R | 54 - act-1.0/act/R/search_meta.R |only act-1.0/act/R/search_new.R | 108 ++- act-1.0/act/R/search_openresult_inpraat.R |only act-1.0/act/R/search_openresult_inquicktime.R |only act-1.0/act/R/search_playresults_inquicktime.R |only act-1.0/act/R/search_run.R | 150 +--- act-1.0/act/R/search_sub.R | 49 - act-1.0/act/R/search_transcript_content.R | 104 +-- act-1.0/act/R/search_transcript_fulltext.R | 228 +----- act-1.0/act/R/tiers____________________________.R |only act-1.0/act/R/tiers_all.R |only act-1.0/act/R/tiers_convert.R |only act-1.0/act/R/tiers_rename.R |only act-1.0/act/R/tiers_sort.R |only act-1.0/act/R/transcript________________________.R |only act-1.0/act/R/transcripts_add.R |only act-1.0/act/R/transcripts_cure.R |only act-1.0/act/R/transcripts_cure_single.R |only act-1.0/act/R/transcripts_delete.R |only act-1.0/act/R/transcripts_filter.R |only act-1.0/act/R/transcripts_filter_single.R |only act-1.0/act/R/transcripts_merge.R |only act-1.0/act/R/transcripts_rename.R |only act-1.0/act/R/transcripts_update_fulltexts.R |only act-1.0/act/R/transcripts_update_normalization.R |only act-1.0/act/data/examplecorpus.RData |binary act-1.0/act/inst/examples/act-package.R | 29 act-1.0/act/inst/examples/annotations__EX_______________________.R |only act-1.0/act/inst/examples/annotations_delete.R |only act-1.0/act/inst/examples/annotations_delete_empty.R |only act-1.0/act/inst/examples/annotations_matrix.R |only act-1.0/act/inst/examples/annotations_replace_copy.R |only act-1.0/act/inst/examples/class_________EX_______________________.R |only act-1.0/act/inst/examples/corpus_______EX________________________.R |only act-1.0/act/inst/examples/corpus_export.R |only act-1.0/act/inst/examples/corpus_import.R |only act-1.0/act/inst/examples/corpus_new.R | 6 act-1.0/act/inst/examples/export_eaf.R |only act-1.0/act/inst/examples/export_exb.R |only act-1.0/act/inst/examples/export_printtranscript.R |only act-1.0/act/inst/examples/export_rpraat.R |only act-1.0/act/inst/examples/export_srt.R |only act-1.0/act/inst/examples/export_textgrid.R |only act-1.0/act/inst/examples/helper________EX________________________.R |only act-1.0/act/inst/examples/helper_tiers_merge_tables.R |only act-1.0/act/inst/examples/helper_tiers_new_table.R |only act-1.0/act/inst/examples/helper_tiers_sort_table.R |only act-1.0/act/inst/examples/helper_transcriptNames_get.R |only act-1.0/act/inst/examples/helper_transcriptNames_make.R |only act-1.0/act/inst/examples/helper_transcriptNames_set.R |only act-1.0/act/inst/examples/import.R |only act-1.0/act/inst/examples/import_eaf.R |only act-1.0/act/inst/examples/import_exb.R |only act-1.0/act/inst/examples/import_rpraat.R |only act-1.0/act/inst/examples/import_textgrid.R |only act-1.0/act/inst/examples/matrix________EX________________________.R |only act-1.0/act/inst/examples/matrix_load.R | 3 act-1.0/act/inst/examples/matrix_save.R | 2 act-1.0/act/inst/examples/media_________EX________________________.R |only act-1.0/act/inst/examples/media_assign.R | 2 act-1.0/act/inst/examples/media_getPathToExistingFile.R |only act-1.0/act/inst/examples/search_________EX________________________.R |only act-1.0/act/inst/examples/search_concordance.R | 12 act-1.0/act/inst/examples/search_cuts_media.R |only act-1.0/act/inst/examples/search_cuts_printtranscript.R |only act-1.0/act/inst/examples/search_cuts_srt.R |only act-1.0/act/inst/examples/search_meta.R |only act-1.0/act/inst/examples/search_openresult_inquicktime.R |only act-1.0/act/inst/examples/search_playresults_inquicktime.R |only act-1.0/act/inst/examples/search_run.R | 14 act-1.0/act/inst/examples/search_transcript_content.R | 3 act-1.0/act/inst/examples/tiers____________EX______________________.R |only act-1.0/act/inst/examples/tiers_convert.R |only act-1.0/act/inst/examples/tiers_rename.R |only act-1.0/act/inst/examples/tiers_sort.R |only act-1.0/act/inst/examples/transcript________EX______________________.R |only act-1.0/act/inst/examples/transcripts_add.R |only act-1.0/act/inst/examples/transcripts_cure.R |only act-1.0/act/inst/examples/transcripts_cure_single.R |only act-1.0/act/inst/examples/transcripts_delete.R |only act-1.0/act/inst/examples/transcripts_filter.R |only act-1.0/act/inst/examples/transcripts_filter_single.R |only act-1.0/act/inst/examples/transcripts_merge.R |only act-1.0/act/inst/examples/transcripts_rename.R |only act-1.0/act/inst/extdata/applescript |only act-1.0/act/inst/extdata/examplecorpus/gat/BOL_CCBA_SP_MeryGaby2.TextGrid | 2 act-1.0/act/inst/extdata/examplecorpus/sync/SYNC_rotar_y_flexionar.eaf |only act-1.0/act/inst/extdata/normalization/normalizationMatrix.csv | 2 act-1.0/act/inst/extdata/praat/OpenSelectionInPraat.praat | 10 act-1.0/act/man/act.Rd | 113 --- act-1.0/act/man/annotations_all.Rd |only act-1.0/act/man/annotations_delete.Rd |only act-1.0/act/man/annotations_delete_empty.Rd |only act-1.0/act/man/annotations_matrix.Rd |only act-1.0/act/man/annotations_replace_copy.Rd |only act-1.0/act/man/corpus-class.Rd |only act-1.0/act/man/corpus_export.Rd |only act-1.0/act/man/corpus_import.Rd |only act-1.0/act/man/corpus_new.Rd | 71 +- act-1.0/act/man/examplecorpus.Rd | 2 act-1.0/act/man/export_eaf.Rd |only act-1.0/act/man/export_exb.Rd |only act-1.0/act/man/export_printtranscript.Rd |only act-1.0/act/man/export_rpraat.Rd |only act-1.0/act/man/export_srt.Rd |only act-1.0/act/man/export_textgrid.Rd |only act-1.0/act/man/helper_format_time.Rd |only act-1.0/act/man/helper_tiers_merge_tables.Rd |only act-1.0/act/man/helper_tiers_new_table.Rd |only act-1.0/act/man/helper_tiers_sort_table.Rd |only act-1.0/act/man/helper_transcriptNames_get.Rd |only act-1.0/act/man/helper_transcriptNames_make.Rd |only act-1.0/act/man/helper_transcriptNames_set.Rd |only act-1.0/act/man/import.Rd |only act-1.0/act/man/import_eaf.Rd |only act-1.0/act/man/import_exb.Rd |only act-1.0/act/man/import_rpraat.Rd |only act-1.0/act/man/import_textgrid.Rd |only act-1.0/act/man/info.Rd |only act-1.0/act/man/info_summarized.Rd |only act-1.0/act/man/layout-class.Rd |only act-1.0/act/man/matrix_load.Rd | 9 act-1.0/act/man/matrix_save.Rd | 4 act-1.0/act/man/media_assign.Rd | 28 act-1.0/act/man/media_delete.Rd |only act-1.0/act/man/media_getPathToExistingFile.Rd |only act-1.0/act/man/options_delete.Rd |only act-1.0/act/man/options_show.Rd |only act-1.0/act/man/search-class.Rd |only act-1.0/act/man/search_concordance.Rd | 26 act-1.0/act/man/search_cuts_media.Rd |only act-1.0/act/man/search_cuts_printtranscript.Rd |only act-1.0/act/man/search_cuts_srt.Rd |only act-1.0/act/man/search_meta.Rd |only act-1.0/act/man/search_new.Rd | 65 + act-1.0/act/man/search_openresult_inpraat.Rd |only act-1.0/act/man/search_openresult_inquicktime.Rd |only act-1.0/act/man/search_playresults_inquicktime.Rd |only act-1.0/act/man/search_results_export.Rd | 2 act-1.0/act/man/search_results_import.Rd | 4 act-1.0/act/man/search_run.Rd | 23 act-1.0/act/man/search_searchandopen_inpraat.Rd |only act-1.0/act/man/search_sub.Rd | 15 act-1.0/act/man/search_transcript_content.Rd | 25 act-1.0/act/man/search_transcript_fulltext.Rd | 4 act-1.0/act/man/tiers_all.Rd |only act-1.0/act/man/tiers_convert.Rd |only act-1.0/act/man/tiers_rename.Rd |only act-1.0/act/man/tiers_sort.Rd |only act-1.0/act/man/transcript-class.Rd |only act-1.0/act/man/transcripts_add.Rd |only act-1.0/act/man/transcripts_cure.Rd |only act-1.0/act/man/transcripts_cure_single.Rd |only act-1.0/act/man/transcripts_delete.Rd |only act-1.0/act/man/transcripts_filter.Rd |only act-1.0/act/man/transcripts_filter_single.Rd |only act-1.0/act/man/transcripts_merge.Rd |only act-1.0/act/man/transcripts_rename.Rd |only act-1.0/act/man/transcripts_update_fulltexts.Rd |only act-1.0/act/man/transcripts_update_normalization.Rd |only 289 files changed, 1282 insertions(+), 1111 deletions(-)
Title: Soil Hydraulic Properties
Description: Provides functions for (1) soil water retention (SWC) and unsaturated hydraulic conductivity (Ku) (van Genuchten-Mualem (vGM or vG) [1, 2], Peters-Durner-Iden (PDI) [3, 4, 5], Brooks and Corey (bc) [8]), (2) fitting of parameter for SWC and/or Ku using Shuffled Complex Evolution (SCE) optimisation and (3) calculation of soil hydraulic properties (Ku and soil water contents) based on the simplified evaporation method (SEM) [6, 7].
Main references:
[1] van Genuchten (1980) <doi:10.2136/sssaj1980.03615995004400050002x>,
[2] Mualem (1976) <doi:10.1029/WR012i003p00513>,
[3] Peters (2013) <doi:10.1002/wrcr.20548>,
[4] Iden and Durner (2013) <doi:10.1002/2014WR015937>,
[5] Peters (2014) <doi:10.1002/2014WR015937>,
[6] Wind G. P. (1966),
[7] Peters and Durner (2008) <doi:10.1016/j.jhydrol.2008.04.016> and
[8] Brooks and Corey (1964).
Author: Ullrich Dettmann [aut, cre],
Felix Andrews [ctb] (For the code copied from the hydromad::SCEoptim
function (Version: 0.9-15) which is not on r-cran
(https://github.com/floybix/hydromad). The SCEoptim function is
adapted, and substantially revised from Brecht Donckels MATLAB code
which is in turn adopted from Qingyun Duans MATLAB code),
Brecht Donckels [ctb] (For the Matlab code which was adapted and
reviesed in the hydromad::SCEoptim function.),
Qingyun Duan [ctb] (For the MATLAB code adapted from Brecht Donkels.)
Maintainer: Ullrich Dettmann <ullrich.dettmann@thuenen.de>
Diff between SoilHyP versions 0.1.4 dated 2020-05-19 and 0.1.5 dated 2021-01-08
SoilHyP-0.1.4/SoilHyP/data/dataSEM_old.RData |only SoilHyP-0.1.5/SoilHyP/DESCRIPTION | 14 +++++++------- SoilHyP-0.1.5/SoilHyP/MD5 | 15 +++++++++------ SoilHyP-0.1.5/SoilHyP/NAMESPACE | 4 ++++ SoilHyP-0.1.5/SoilHyP/R/DK_to_SWC.R |only SoilHyP-0.1.5/SoilHyP/R/calcKS.r |only SoilHyP-0.1.5/SoilHyP/man/DK_to_SWC.Rd |only SoilHyP-0.1.5/SoilHyP/man/calcKS.Rd |only SoilHyP-0.1.5/SoilHyP/man/dataSEM.Rd | 4 +++- SoilHyP-0.1.5/SoilHyP/man/dataSHP.Rd | 4 +++- SoilHyP-0.1.5/SoilHyP/man/dataTestthat.Rd | 4 +++- 11 files changed, 29 insertions(+), 16 deletions(-)
Title: Translate Models from System Dynamics Software into 'R'
Description: The goal of 'readsdr' is to bridge the design capabilities from
specialised System Dynamics software with the powerful numerical tools
offered by 'R' libraries. The package accomplishes this goal by parsing
'XMILE' files ('Vensim' and 'Stella') models into 'R' objects to construct
networks (graph theory); 'ODE' functions for 'Stan'; and inputs to simulate
via 'deSolve' as described in Duggan (2016) <doi:10.1007/978-3-319-34043-2>.
Author: Jair Andrade [aut, cre] (<https://orcid.org/0000-0002-1412-7868>)
Maintainer: Jair Andrade <jair.albert.andrade@gmail.com>
Diff between readsdr versions 0.1.0 dated 2020-06-12 and 0.2.0 dated 2021-01-08
DESCRIPTION | 8 MD5 | 73 ++-- NAMESPACE | 8 NEWS.md |only R/create_stan_function.R | 85 +---- R/generate_igraph_inputs.R | 3 R/if_else_funs.R | 19 + R/math_funs.R |only R/read_xmile.R | 44 ++ R/simulators.R | 228 +++++++++++++ R/stan_ode_function.R |only R/stan_utils.R |only R/stat_funs.R |only R/summaries.R |only R/translate_smooth.R |only R/utils.R | 6 R/var_consts_xmile.R |only R/xmile_helpers.R | 53 ++- R/xml_model_components.R | 194 +++++------ README.md | 40 +- build/vignette.rds |binary inst/doc/Introduction_to_readsdr.Rmd | 10 inst/doc/Introduction_to_readsdr.html | 236 +++++++++----- man/create_stan_function.Rd | 13 man/extract_timeseries_stock.Rd |only man/extract_timeseries_var.Rd |only man/read_xmile.Rd | 8 man/sd_constants.Rd |only man/sd_sensitivity_run.Rd |only man/sd_stocks.Rd |only man/stan_data.Rd |only man/stan_ode_function.Rd |only man/stan_transformed_data.Rd |only tests/testthat/test-create_stan_function.R | 139 ++++---- tests/testthat/test-generate_deSolve_components.R | 4 tests/testthat/test-if_else_funs.R | 21 + tests/testthat/test-math_funs.R |only tests/testthat/test-read_xmile.R | 50 ++- tests/testthat/test-simulators.R | 104 ++++++ tests/testthat/test-stan_ode_function.R |only tests/testthat/test-stan_utils.R |only tests/testthat/test-stat_funs.R |only tests/testthat/test-summaries.R |only tests/testthat/test-translate_SMOOTH.R |only tests/testthat/test-var_consts_xmile.R |only tests/testthat/test-xmile_graph_funs.R | 3 tests/testthat/test-xmile_helpers.R | 23 + tests/testthat/test-xml_model_components.R | 360 +++++++++------------- vignettes/Introduction_to_readsdr.Rmd | 10 49 files changed, 1143 insertions(+), 599 deletions(-)
Title: Ridgeline Plots in 'ggplot2'
Description: Ridgeline plots provide a convenient way of visualizing changes in distributions over time or space. This package enables the creation of such plots in 'ggplot2'.
Author: Claus O. Wilke [aut, cre] (<https://orcid.org/0000-0002-7470-9261>)
Maintainer: Claus O. Wilke <wilke@austin.utexas.edu>
Diff between ggridges versions 0.5.2 dated 2020-01-12 and 0.5.3 dated 2021-01-08
DESCRIPTION | 10 MD5 | 47 NEWS.md | 5 README.md | 51 build/vignette.rds |binary inst/doc/gallery.Rmd | 8 inst/doc/gallery.html | 351 +++--- inst/doc/introduction.html | 551 +++++----- man/Aus_athletes.Rd | 4 man/Catalan_elections.Rd | 6 man/figures/README-diamonds-1.png |binary man/lincoln_weather.Rd | 6 man/stat_binline.Rd | 16 tests/figs/deps.txt | 2 tests/figs/geom-gradient/geom-density-ridges-gradient-continuous-fill.svg | 32 tests/figs/geom-gradient/geom-density-ridges-gradient-ecdf-fill.svg | 26 tests/figs/geom-gradient/geom-density-ridges-gradient-jittered-points-can-be-turned-on.svg | 32 tests/testthat/Rplots.pdf |binary tests/testthat/helper-vdiffr.R |only tests/testthat/test_geom_density_ridges.R | 8 tests/testthat/test_geom_gradient.R | 14 tests/testthat/test_geom_vridgeline.R | 4 tests/testthat/test_scale_cyclical.R | 4 tests/testthat/test_theme_ridges.R | 6 vignettes/gallery.Rmd | 8 25 files changed, 616 insertions(+), 575 deletions(-)
Title: Circular Visualization
Description: Circular layout is an efficient way for the visualization of huge
amounts of information. Here this package provides an implementation
of circular layout generation in R as well as an enhancement of available
software. The flexibility of the package is based on the usage of low-level
graphics functions such that self-defined high-level graphics can be easily
implemented by users for specific purposes. Together with the seamless
connection between the powerful computational and visual environment in R,
it gives users more convenience and freedom to design figures for
better understanding complex patterns behind multiple dimensional data.
The package is described in Gu et al. 2014 <doi:10.1093/bioinformatics/btu393>.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between circlize versions 0.4.11 dated 2020-10-31 and 0.4.12 dated 2021-01-08
DESCRIPTION | 10 - LICENSE | 2 MD5 | 42 ++-- NAMESPACE | 5 NEWS | 19 ++ R/chordDiagram.R | 10 - R/circos.heatmap.R | 209 +++++++++++++++++----- R/genomic.R | 37 ++- R/genomic_utils.R | 20 ++ R/global.R | 3 R/link.R | 153 +++++++++++++--- R/low_level.R | 369 ++++++++++++++++++++++++++++++++++++++- R/utils.R | 5 man/Subset.CELL_META.Rd | 2 man/arrange_links_evenly.Rd |only man/chordDiagramFromDataFrame.Rd | 2 man/circos.boxplot.Rd | 2 man/circos.connect.Rd |only man/circos.genomicLabels.Rd | 4 man/circos.heatmap.Rd | 5 man/circos.heatmap.initialize.Rd | 6 man/circos.labels.Rd |only man/circos.link.Rd | 2 man/get_most_inside_radius.Rd |only 24 files changed, 784 insertions(+), 123 deletions(-)
Title: Entropy-Based Segregation Indices
Description: Computes entropy-based segregation indices, as developed by
Theil (1971) <isbn:978-0471858454>, with a focus on
the Mutual Information Index (M) and Theil's Information Index (H).
The M, further described by Mora and Ruiz-Castillo (2011) <doi:10.1111/j.1467-9531.2011.01237.x>
and Frankel and Volij (2011) <doi:10.1016/j.jet.2010.10.008>,
is a measure of segregation that is highly decomposable. The package provides
tools to decompose the index by units and groups (local segregation),
and by within and between terms.
Includes standard error estimation by bootstrapping.
Author: Benjamin Elbers [aut, cre] (<https://orcid.org/0000-0001-5392-3448>)
Maintainer: Benjamin Elbers <be2239@columbia.edu>
Diff between segregation versions 0.3.0 dated 2019-09-20 and 0.4.0 dated 2021-01-08
segregation-0.3.0/segregation/tests/testthat/test_lintr.R |only segregation-0.4.0/segregation/DESCRIPTION | 14 segregation-0.4.0/segregation/MD5 | 46 +- segregation-0.4.0/segregation/NAMESPACE | 1 segregation-0.4.0/segregation/NEWS.md | 7 segregation-0.4.0/segregation/R/ipf.R | 10 segregation-0.4.0/segregation/R/mutual.R | 168 +++++----- segregation-0.4.0/segregation/R/mutual_difference.R | 52 +-- segregation-0.4.0/segregation/R/mutual_expected.R |only segregation-0.4.0/segregation/R/segregation.R | 17 - segregation-0.4.0/segregation/README.md | 62 ++- segregation-0.4.0/segregation/man/ipf.Rd | 11 segregation-0.4.0/segregation/man/mutual_difference.Rd | 28 + segregation-0.4.0/segregation/man/mutual_expected.Rd |only segregation-0.4.0/segregation/man/mutual_local.Rd | 20 - segregation-0.4.0/segregation/man/mutual_total.Rd | 20 - segregation-0.4.0/segregation/man/mutual_within.Rd | 21 - segregation-0.4.0/segregation/man/schools00.Rd | 6 segregation-0.4.0/segregation/man/schools05.Rd | 6 segregation-0.4.0/segregation/man/segregation.Rd | 1 segregation-0.4.0/segregation/tests/testthat/test_ipf.R | 4 segregation-0.4.0/segregation/tests/testthat/test_mutual_difference.R | 18 - segregation-0.4.0/segregation/tests/testthat/test_mutual_expected.R |only segregation-0.4.0/segregation/tests/testthat/test_mutual_local.R | 12 segregation-0.4.0/segregation/tests/testthat/test_mutual_total.R | 18 - segregation-0.4.0/segregation/tests/testthat/test_mutual_within.R | 14 26 files changed, 346 insertions(+), 210 deletions(-)
Title: Basic Functions for Supporting an Implementation of Choice
Experiments
Description: Provides basic functions that support an implementation of (discrete) choice experiments (CEs). CEs is a question-based survey method measuring people's preferences for goods/services and their characteristics. Refer to Louviere et al. (2000) <doi:10.1017/CBO9780511753831> for details on CEs, and Aizaki (2012) <doi:10.18637/jss.v050.c02> for the package.
Author: Hideo Aizaki
Maintainer: Hideo Aizaki <azk-r@spa.nifty.com>
Diff between support.CEs versions 0.4-1 dated 2015-08-27 and 0.5-0 dated 2021-01-08
support.CEs-0.4-1/support.CEs/R/print.sb.R |only support.CEs-0.4-1/support.CEs/R/print.summary.sb.R |only support.CEs-0.4-1/support.CEs/R/sb.check.args.R |only support.CEs-0.4-1/support.CEs/R/sb.design.R |only support.CEs-0.4-1/support.CEs/R/sb.extract.R |only support.CEs-0.4-1/support.CEs/R/sb.submit.R |only support.CEs-0.4-1/support.CEs/R/summary.sb.R |only support.CEs-0.4-1/support.CEs/man/sb.design.Rd |only support.CEs-0.5-0/support.CEs/DESCRIPTION | 12 ++-- support.CEs-0.5-0/support.CEs/MD5 | 42 ++++++--------- support.CEs-0.5-0/support.CEs/NAMESPACE | 13 +--- support.CEs-0.5-0/support.CEs/NEWS | 7 ++ support.CEs-0.5-0/support.CEs/R/mwtp.R | 8 ++ support.CEs-0.5-0/support.CEs/inst/CITATION | 10 +-- support.CEs-0.5-0/support.CEs/man/Lma.design.Rd | 7 -- support.CEs-0.5-0/support.CEs/man/gofm.Rd | 9 --- support.CEs-0.5-0/support.CEs/man/make.dataset.Rd | 7 -- support.CEs-0.5-0/support.CEs/man/make.design.matrix.Rd | 5 - support.CEs-0.5-0/support.CEs/man/mwtp.Rd | 9 --- support.CEs-0.5-0/support.CEs/man/pork.Rd | 2 support.CEs-0.5-0/support.CEs/man/questionnaire.Rd | 3 - support.CEs-0.5-0/support.CEs/man/rice.Rd | 2 support.CEs-0.5-0/support.CEs/man/rotation.design.Rd | 5 - support.CEs-0.5-0/support.CEs/man/rural.Rd | 2 support.CEs-0.5-0/support.CEs/man/support.CEs-package.Rd | 20 ++++++- support.CEs-0.5-0/support.CEs/man/syn.res.Rd | 5 - 26 files changed, 73 insertions(+), 95 deletions(-)
Title: Fitting Linear and Generalized Linear Models to Large Data Sets
Description: Fitting linear models and generalized linear models to large data sets by updating algorithms.
Author: Marco Enea [aut, cre],
Ronen Meiri [ctb] (on behalf of DMWay Analytics LTD),
Tomer Kalimi [ctb] (on behalf of DMWay Analytics LTD)
Maintainer: Marco Enea <emarco76@libero.it>
Diff between speedglm versions 0.3-2 dated 2017-01-09 and 0.3-3 dated 2021-01-08
DESCRIPTION | 12 +- MD5 | 22 ++-- NAMESPACE | 49 +++++---- NEWS | 16 +++ R/predict.r | 2 R/speedglm.r | 257 ++++++++++++++++++++++++++++++--------------------- R/speedlm.R | 56 ++++++++--- R/summary.speedglm.r | 51 +++++----- R/summary.speedlm.R | 5 R/uncommented.r | 12 ++ man/speedglm.Rd | 2 man/speedlm.Rd | 7 - 12 files changed, 303 insertions(+), 188 deletions(-)
Title: Power and Sample Size Calculation for Survival Analysis of
Epidemiological Studies
Description: Functions to calculate power and
sample size for testing main effect or interaction effect in
the survival analysis of epidemiological studies
(non-randomized studies), taking into account the
correlation between the covariate of the
interest and other covariates. Some calculations also take
into account the competing risks and stratified analysis.
This package also includes
a set of functions to calculate power and sample size
for testing main effect in the survival analysis of
randomized clinical trials.
Author: Weiliang Qiu, Jorge Chavarro, Ross Lazarus, Bernard Rosner, Jing Ma.
Maintainer: Weiliang Qiu <weiliang.qiu@gmail.com>
Diff between powerSurvEpi versions 0.1.0 dated 2018-02-07 and 0.1.1 dated 2021-01-08
DESCRIPTION | 14 ++++----- MD5 | 60 ++++++++++++++++++++-------------------- NEWS | 54 ++++++++++++++++++++---------------- R/power.stratify.R | 5 ++- R/powerCT.R | 13 +++++--- R/powerEpi.R | 65 +++++++++++++++++++++++++------------------- man/numDEpi.Rd | 24 ++++++++++------ man/numDEpi.default.Rd | 25 ++++++++++------ man/power.stratify.Rd | 34 +++++++++++------------ man/powerCT.Rd | 25 +++++++++++----- man/powerCT.default.Rd | 29 ++++++++++++------- man/powerCT.default0.Rd | 20 ++++++++----- man/powerEpi.Rd | 14 ++++----- man/powerEpi.default.Rd | 29 ++++++++++++------- man/powerEpiCont.Rd | 30 +++++++++++++------- man/powerEpiCont.default.Rd | 29 ++++++++++++------- man/powerEpiInt.Rd | 28 ++++++++++++------ man/powerEpiInt.default0.Rd | 33 ++++++++++++++-------- man/powerEpiInt.default1.Rd | 38 ++++++++++++++++--------- man/powerEpiInt2.Rd | 37 ++++++++++++++++--------- man/ssize.stratify.Rd | 28 +++++++++--------- man/ssizeCT.Rd | 25 +++++++++++----- man/ssizeCT.default.Rd | 29 ++++++++++++------- man/ssizeEpi.Rd | 29 ++++++++++++------- man/ssizeEpi.default.Rd | 29 ++++++++++++------- man/ssizeEpiCont.Rd | 30 +++++++++++++------- man/ssizeEpiCont.default.Rd | 29 ++++++++++++------- man/ssizeEpiInt.Rd | 28 ++++++++++++------ man/ssizeEpiInt.default0.Rd | 33 ++++++++++++++-------- man/ssizeEpiInt.default1.Rd | 36 ++++++++++++++++-------- man/ssizeEpiInt2.Rd | 37 ++++++++++++++++--------- 31 files changed, 588 insertions(+), 351 deletions(-)
Title: Toolbox for Model Building and Forecasting
Description: Implements functions and instruments for regression model building and its
application to forecasting. The main scope of the package is in variables selection
and models specification for cases of time series data. This includes promotional
modelling, selection between different dynamic regressions with non-standard
distributions of errors, selection based on cross validation, solutions to the fat
regression model problem and more. Models developed in the package are tailored
specifically for forecasting purposes. So as a results there are several methods
that allow producing forecasts from these models and visualising them.
Author: Ivan Svetunkov [aut, cre] (Lecturer at Centre for Marketing Analytics
and Forecasting, Lancaster University, UK),
Yves R. Sagaert [ctb] (Visiting Research at Centre for Marketing
Analytics and Forecasting, Lancaster University, UK)
Maintainer: Ivan Svetunkov <ivan@svetunkov.ru>
Diff between greybox versions 0.6.4 dated 2020-12-01 and 0.6.6 dated 2021-01-08
greybox-0.6.4/greybox/man/alaplace-distribution.Rd |only greybox-0.6.4/greybox/man/bcnorm-distribution.Rd |only greybox-0.6.4/greybox/man/fnorm-distribution.Rd |only greybox-0.6.4/greybox/man/laplace-distribution.Rd |only greybox-0.6.4/greybox/man/logitnorm-distribution.Rd |only greybox-0.6.4/greybox/man/s-distribution.Rd |only greybox-0.6.4/greybox/man/tplnorm-distribution.Rd |only greybox-0.6.6/greybox/DESCRIPTION | 10 greybox-0.6.6/greybox/MD5 | 89 +-- greybox-0.6.6/greybox/NAMESPACE | 8 greybox-0.6.6/greybox/NEWS | 26 greybox-0.6.6/greybox/R/alaplace.R | 14 greybox-0.6.6/greybox/R/alm.R | 83 +- greybox-0.6.6/greybox/R/bcnorm.R | 9 greybox-0.6.6/greybox/R/coefbootstrap.R | 2 greybox-0.6.6/greybox/R/determination.R | 16 greybox-0.6.6/greybox/R/error-measures.R | 8 greybox-0.6.6/greybox/R/fnorm.R | 9 greybox-0.6.6/greybox/R/gnorm.R | 235 +++++--- greybox-0.6.6/greybox/R/laplace.R | 10 greybox-0.6.6/greybox/R/logitnorm.R | 9 greybox-0.6.6/greybox/R/methods.R | 246 ++++++-- greybox-0.6.6/greybox/R/ro.R | 2 greybox-0.6.6/greybox/R/svet.R | 10 greybox-0.6.6/greybox/R/temporaldummy.R | 75 +- greybox-0.6.6/greybox/R/tplnorm.R | 11 greybox-0.6.6/greybox/R/xregExpander.R | 31 - greybox-0.6.6/greybox/README.md | 9 greybox-0.6.6/greybox/build/partial.rdb |binary greybox-0.6.6/greybox/inst/doc/alm.R |only greybox-0.6.6/greybox/inst/doc/alm.Rmd | 128 ++-- greybox-0.6.6/greybox/inst/doc/alm.html | 560 ++++++++++++++++++-- greybox-0.6.6/greybox/inst/doc/greybox.Rmd | 15 greybox-0.6.6/greybox/inst/doc/greybox.html | 234 +++++--- greybox-0.6.6/greybox/inst/doc/maUsingGreybox.html | 52 + greybox-0.6.6/greybox/inst/doc/ro.html | 62 +- greybox-0.6.6/greybox/man/ALaplace.Rd |only greybox-0.6.6/greybox/man/BCNormal.Rd |only greybox-0.6.6/greybox/man/FNormal.Rd |only greybox-0.6.6/greybox/man/Laplace.Rd |only greybox-0.6.6/greybox/man/LogitNormal.Rd |only greybox-0.6.6/greybox/man/SDistribution.Rd |only greybox-0.6.6/greybox/man/TPLNormal.Rd |only greybox-0.6.6/greybox/man/alm.Rd | 43 - greybox-0.6.6/greybox/man/coefbootstrap.Rd | 2 greybox-0.6.6/greybox/man/error-measures.Rd | 4 greybox-0.6.6/greybox/man/gnorm.Rd |only greybox-0.6.6/greybox/man/hm.Rd | 2 greybox-0.6.6/greybox/man/measures.Rd | 2 greybox-0.6.6/greybox/man/ro.Rd | 2 greybox-0.6.6/greybox/man/temporaldummy.Rd | 20 greybox-0.6.6/greybox/vignettes/alm.Rmd | 128 ++-- greybox-0.6.6/greybox/vignettes/greybox.Rmd | 15 53 files changed, 1560 insertions(+), 621 deletions(-)
Title: Bayesian Model Averaging for Random and Fixed Effects
Meta-Analysis
Description: Computes the posterior model probabilities for standard meta-analysis models
(null model vs. alternative model assuming either fixed- or random-effects, respectively).
These posterior probabilities are used to estimate the overall mean effect size
as the weighted average of the mean effect size estimates of the random- and
fixed-effect model as proposed by Gronau, Van Erp, Heck, Cesario, Jonas, &
Wagenmakers (2017, <doi:10.1080/23743603.2017.1326760>). The user can define
a wide range of non-informative or informative priors for the mean effect size
and the heterogeneity coefficient. Moreover, using pre-compiled Stan models,
meta-analysis with continuous and discrete moderators with Jeffreys-Zellner-Siow (JZS)
priors can be fitted and tested. This allows to compute Bayes factors and
perform Bayesian model averaging across random- and fixed-effects meta-analysis
with and without moderators. For a primer on Bayesian model-averaged meta-analysis,
see Gronau, Heck, Berkhout, Haaf, & Wagenmakers (2020, <doi:10.31234/osf.io/97qup>).
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>),
Quentin F. Gronau [ctb],
Eric-Jan Wagenmakers [ctb]
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>
Diff between metaBMA versions 0.6.5 dated 2020-10-29 and 0.6.6 dated 2021-01-08
metaBMA-0.6.5/metaBMA/R/stanpackage-internal.R |only metaBMA-0.6.5/metaBMA/inst/include/meta_header.hpp |only metaBMA-0.6.5/metaBMA/src/init.cpp |only metaBMA-0.6.5/metaBMA/src/stan_files |only metaBMA-0.6.5/metaBMA/tools |only metaBMA-0.6.6/metaBMA/DESCRIPTION | 19 - metaBMA-0.6.6/metaBMA/MD5 | 153 +++++----- metaBMA-0.6.6/metaBMA/NAMESPACE | 131 ++++---- metaBMA-0.6.6/metaBMA/NEWS | 9 metaBMA-0.6.6/metaBMA/R/bma.R | 4 metaBMA-0.6.6/metaBMA/R/data_facial_feedback.R | 4 metaBMA-0.6.6/metaBMA/R/data_towels.R | 2 metaBMA-0.6.6/metaBMA/R/metaBMA.R | 3 metaBMA-0.6.6/metaBMA/R/meta_bma.R | 13 metaBMA-0.6.6/metaBMA/R/meta_default.R | 109 +++---- metaBMA-0.6.6/metaBMA/R/meta_fixed.R | 9 metaBMA-0.6.6/metaBMA/R/meta_ordered.R | 10 metaBMA-0.6.6/metaBMA/R/meta_random.R | 14 metaBMA-0.6.6/metaBMA/R/meta_stan.R | 6 metaBMA-0.6.6/metaBMA/R/predicted_bf.R | 11 metaBMA-0.6.6/metaBMA/R/prior.R | 13 metaBMA-0.6.6/metaBMA/R/stanmodels.R | 63 +--- metaBMA-0.6.6/metaBMA/R/zzz.R | 9 metaBMA-0.6.6/metaBMA/build/partial.rdb |only metaBMA-0.6.6/metaBMA/configure |only metaBMA-0.6.6/metaBMA/configure.win |only metaBMA-0.6.6/metaBMA/inst/doc/metaBMA.R | 8 metaBMA-0.6.6/metaBMA/inst/doc/metaBMA.Rmd | 10 metaBMA-0.6.6/metaBMA/inst/doc/metaBMA.html | 113 ++++--- metaBMA-0.6.6/metaBMA/inst/include/stan_meta_header.hpp |only metaBMA-0.6.6/metaBMA/inst/stan |only metaBMA-0.6.6/metaBMA/man/bma.Rd | 4 metaBMA-0.6.6/metaBMA/man/facial_feedback.Rd | 4 metaBMA-0.6.6/metaBMA/man/metaBMA-package.Rd | 9 metaBMA-0.6.6/metaBMA/man/meta_bma.Rd | 19 - metaBMA-0.6.6/metaBMA/man/meta_default.Rd | 64 ++-- metaBMA-0.6.6/metaBMA/man/meta_fixed.Rd | 6 metaBMA-0.6.6/metaBMA/man/meta_ordered.Rd | 12 metaBMA-0.6.6/metaBMA/man/meta_random.Rd | 16 - metaBMA-0.6.6/metaBMA/man/plot_default.Rd | 11 metaBMA-0.6.6/metaBMA/man/power_pose.Rd | 2 metaBMA-0.6.6/metaBMA/man/prior.Rd | 9 metaBMA-0.6.6/metaBMA/man/towels.Rd | 2 metaBMA-0.6.6/metaBMA/src/Makevars | 23 - metaBMA-0.6.6/metaBMA/src/Makevars.win | 27 - metaBMA-0.6.6/metaBMA/src/RcppExports.cpp |only metaBMA-0.6.6/metaBMA/src/stanExports_fixed.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_fixed.h |only metaBMA-0.6.6/metaBMA/src/stanExports_fixed_jzs.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_fixed_jzs.h |only metaBMA-0.6.6/metaBMA/src/stanExports_random.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_random.h |only metaBMA-0.6.6/metaBMA/src/stanExports_random_H0.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_random_H0.h |only metaBMA-0.6.6/metaBMA/src/stanExports_random_dstudy.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_random_dstudy.h |only metaBMA-0.6.6/metaBMA/src/stanExports_random_jzs.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_random_jzs.h |only metaBMA-0.6.6/metaBMA/src/stanExports_random_jzs_dstudy.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_random_jzs_dstudy.h |only metaBMA-0.6.6/metaBMA/src/stanExports_random_ordered.cc |only metaBMA-0.6.6/metaBMA/src/stanExports_random_ordered.h |only metaBMA-0.6.6/metaBMA/tests/testthat/test_H0_logml.R | 16 - metaBMA-0.6.6/metaBMA/tests/testthat/test_bma.R | 9 metaBMA-0.6.6/metaBMA/tests/testthat/test_data_frame_evaluation.R | 24 - metaBMA-0.6.6/metaBMA/tests/testthat/test_gronau2017powerpose.R | 22 - metaBMA-0.6.6/metaBMA/tests/testthat/test_integrate.R | 34 +- metaBMA-0.6.6/metaBMA/tests/testthat/test_jzs.R | 28 + metaBMA-0.6.6/metaBMA/tests/testthat/test_prior.R | 3 metaBMA-0.6.6/metaBMA/vignettes/metaBMA.Rmd | 10 70 files changed, 555 insertions(+), 512 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-10-29 0.8.3
2020-03-13 0.8.0
2019-08-06 0.7.2
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-02-08 1.0.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-05-23 0.1.1
2020-05-08 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-11-15 0.1.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-07-07 1.0.2
Title: Hierarchical Multinomial Processing Tree Modeling
Description: User-friendly analysis of hierarchical multinomial processing tree (MPT)
models that are often used in cognitive psychology. Implements the latent-trait
MPT approach (Klauer, 2010) <DOI:10.1007/s11336-009-9141-0> and the beta-MPT
approach (Smith & Batchelder, 2010) <DOI:10.1016/j.jmp.2009.06.007> to model
heterogeneity of participants. MPT models are conveniently specified by an
.eqn-file as used by other MPT software and data are provided by a .csv-file
or directly in R. Models are either fitted by calling JAGS or by an MPT-tailored
Gibbs sampler in C++ (only for nonhierarchical and beta MPT models). Provides
tests of heterogeneity and MPT-tailored summaries and plotting functions.
A detailed documentation is available in Heck, Arnold, & Arnold (2018)
<DOI:10.3758/s13428-017-0869-7>.
Author: Daniel W. Heck [aut, cre] (<https://orcid.org/0000-0002-6302-9252>),
Nina R. Arnold [aut, dtc],
Denis Arnold [aut],
Alexander Ly [ctb],
Marius Barth [ctb] (<https://orcid.org/0000-0002-3421-6665>)
Maintainer: Daniel W. Heck <dheck@uni-marburg.de>
Diff between TreeBUGS versions 1.4.5 dated 2020-05-31 and 1.4.7 dated 2021-01-08
DESCRIPTION | 14 +-- MD5 | 37 ++++---- NEWS | 7 + R/BF_Rao_Blackwell.R | 3 R/correlationBayesMCMC.R | 8 - R/plotFit.R | 9 +- R/testHetChi.R | 2 R/testHetPerm.R | 2 build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 2 inst/doc/TreeBUGS_1_intro.Rmd | 14 +-- inst/doc/TreeBUGS_1_intro.html | 162 +++++++++++++++++++++----------------- inst/doc/TreeBUGS_2_extended.html | 124 +++++++++++++++++------------ man/TreeBUGS-package.Rd | 2 man/correlationPosterior.Rd | 8 - man/plotFit.Rd | 2 man/testHetChi.Rd | 2 man/testHetPerm.Rd | 2 vignettes/TreeBUGS_1_intro.Rmd | 14 +-- 20 files changed, 236 insertions(+), 178 deletions(-)
More information about RandomForestsGLS at CRAN
Permanent link
Title: Check the Heaviness of Package Dependencies
Description: It checks the heaviness of the packages that user's
package depends on. For each package listed in the "Depends", "Imports" and
"Suggests" fields in the DESCRIPTION file, it opens a new R session, loads the
package and counts the number of namespaces that are loaded. The summary of
the dependencies is visualized by a customized heatmap. Examples of dependency
analysis can be found at <https://jokergoo.github.io/pkgndep/stat/>.
Author: Zuguang Gu
Maintainer: Zuguang Gu <z.gu@dkfz.de>
Diff between pkgndep versions 1.0.1 dated 2020-11-12 and 1.0.2 dated 2021-01-08
DESCRIPTION | 8 ++++---- LICENSE | 2 +- MD5 | 16 ++++++++-------- R/pkgndep.R | 15 ++++++++------- inst/doc/pkgndep.R | 29 ++++++++++++++++++++++++++++- inst/doc/pkgndep.Rmd | 47 ++++++++++++++++++++++++++++++++++++++++++++++- inst/doc/pkgndep.html | 30 +++++++++++++++++++++--------- man/plot.pkgndep.Rd | 9 +++++---- vignettes/pkgndep.Rmd | 47 ++++++++++++++++++++++++++++++++++++++++++++++- 9 files changed, 167 insertions(+), 36 deletions(-)
Title: Functions and Datasets for the Book by Keon-Woong Moon
Description: Several analysis-related functions for the book entitled "R
statistics and graph for medical articles" (written in Korean), version 1,
by Keon-Woong Moon with Korean demographic data with several plot
functions.
Author: Keon-Woong Moon [aut, cre]
Maintainer: Keon-Woong Moon <cardiomoon@gmail.com>
Diff between moonBook versions 0.2.3 dated 2018-07-23 and 0.2.4 dated 2021-01-08
DESCRIPTION | 13 MD5 | 56 ++-- NEWS | 6 R/addComma.R | 3 R/compressMytable.R | 4 R/mycph.R | 3 R/mycsv.R | 6 R/mytable.R | 2 build/vignette.rds |binary inst/doc/moonBook.R | 42 +-- inst/doc/moonBook.html | 340 ++++++++++++++++--------- inst/doc/moonBook_update.R | 30 +- inst/doc/moonBook_update.html | 562 +++++++++++++++++++++++++----------------- man/HRplot.Rd | 20 + man/ORplot.Rd | 17 + man/ORplot.sub.Rd | 17 + man/acs.Rd | 6 man/addComma.Rd | 3 man/compress.Rd | 4 man/mycsv.Rd | 2 man/mycsv.cbind.mytable.Rd | 2 man/mycsv.mytable.Rd | 2 man/mylatex.Rd | 36 ++ man/mytable.Rd | 2 man/mytable2.Rd | 17 + man/mytable_df.Rd | 12 man/mytable_sub.Rd | 17 + man/mytable_sub2.Rd | 12 man/radial.Rd | 6 29 files changed, 800 insertions(+), 442 deletions(-)
Title: The Genie++ Hierarchical Clustering Algorithm with Noise Points
Detection
Description: A retake on the Genie algorithm - a robust
hierarchical clustering method
(Gagolewski, Bartoszuk, Cena, 2016 <DOI:10.1016/j.ins.2016.05.003>).
Now faster and more memory efficient; determining the whole hierarchy
for datasets of 10M points in low dimensional Euclidean spaces or
100K points in high-dimensional ones takes only 1-2 minutes.
Allows clustering with respect to mutual reachability distances
so that it can act as a noise point detector or a robustified version of
'HDBSCAN*' (that is able to detect a predefined number of
clusters and hence it does not dependent on the somewhat
fragile 'eps' parameter).
The package also features an implementation of economic inequity indices
(the Gini, Bonferroni index) and external cluster validity measures
(partition similarity scores; e.g., the adjusted Rand, Fowlkes-Mallows,
adjusted mutual information, pair sets index).
See also the 'Python' version of 'genieclust' available on 'PyPI', which
supports sparse data, more metrics, and even larger datasets.
Author: Marek Gagolewski [aut, cre, cph]
(<https://orcid.org/0000-0003-0637-6028>),
Maciej Bartoszuk [ctb],
Anna Cena [ctb],
Peter M. Larsen [ctb]
Maintainer: Marek Gagolewski <marek@gagolewski.com>
Diff between genieclust versions 0.9.7 dated 2021-01-07 and 0.9.8 dated 2021-01-08
DESCRIPTION | 8 - MD5 | 14 - NEWS | 29 ++- R/RcppExports.R | 18 +- src/RcppExports.cpp | 76 +++++----- src/r_compare_partitions.cpp | 36 ++-- src/r_emst.cpp | 18 +- src/r_gclust.cpp | 316 ++++++++++++++++++++----------------------- 8 files changed, 255 insertions(+), 260 deletions(-)
Title: Design-Based Global and Small-Area Estimations for Multiphase
Forest Inventories
Description: Extensive global and small-area estimation procedures for multiphase
forest inventories under the design-based Monte-Carlo approach are provided.
The implementation has been published in the Journal of Statistical Software (<doi:10.18637/jss.v097.i04>)
and includes estimators for simple and cluster sampling
published by Daniel Mandallaz in 2007 (<doi:10.1201/9781584889779>),
2013 (<doi:10.1139/cjfr-2012-0381>, <doi:10.1139/cjfr-2013-0181>,
<doi:10.1139/cjfr-2013-0449>, <doi:10.3929/ethz-a-009990020>)
and 2016 (<doi:10.3929/ethz-a-010579388>). It provides point estimates,
their external- and design-based variances and confidence intervals, as well as a
set of functions to analyze and visualize the produced estimates.
The procedures have also been optimized for the use of remote sensing data
as auxiliary information, as demonstrated in 2018 by Hill et al. (<doi:10.3390/rs10071052>).
Author: Andreas Hill [aut, cre],
Alexander Massey [aut],
Daniel Mandallaz [ctb]
Maintainer: Andreas Hill <andreas.hill@wald-rlp.de>
Diff between forestinventory versions 0.3.1 dated 2017-10-16 and 1.0.0 dated 2021-01-08
DESCRIPTION | 37 ++++++++++--------- MD5 | 58 +++++++++++++++--------------- NAMESPACE | 1 NEWS | 3 + NEWS.md |only R/confint_methods.R | 16 +++++--- R/esttable.R | 38 ++++++++++++------- R/forestinventory.R | 5 ++ R/grisons_documentation.R | 2 - R/mphasegain.R | 17 ++++++-- R/onephase.R | 3 + R/plot_methods.R | 22 ++++++++--- R/print_methods.R | 12 +++--- R/summary_methods.R | 11 +++-- R/threephase.R | 7 ++- R/twophase.R | 9 ++-- R/zberg_documentation.R | 6 +-- README.md | 65 +++++++++++++++++++++++++++------- build/partial.rdb |only build/vignette.rds |binary inst/CITATION | 30 ++++++++------- inst/doc/forestinventory_vignette.pdf |binary man/confint.Rd | 12 +++--- man/estTable.Rd | 10 +++-- man/forestinventory.Rd | 6 ++- man/grisons.Rd | 6 ++- man/onephase.Rd | 11 ++++- man/plot.esttable.Rd | 5 +- man/threephase.Rd | 22 ++++++++--- man/twophase.Rd | 24 ++++++++---- man/zberg.Rd | 10 +++-- 31 files changed, 289 insertions(+), 159 deletions(-)
More information about forestinventory at CRAN
Permanent link
Title: Draw Treemaps in 'ggplot2'
Description: Provides 'ggplot2' geoms for drawing treemaps.
Author: David Wilkins [aut, cre],
Bob Rudis [ctb] (<https://orcid.org/0000-0001-5670-2640>)
Maintainer: David Wilkins <david@wilkox.org>
Diff between treemapify versions 2.5.4 dated 2020-11-19 and 2.5.5 dated 2021-01-08
DESCRIPTION | 12 +++++----- MD5 | 13 +++++----- NEWS.md | 7 +++++ R/expect_doppelganger.R |only R/treemap_squarified.R | 2 - inst/WORDLIST | 37 +++++++++++++++---------------- inst/doc/introduction-to-treemapify.html | 4 +-- tests/testthat/test_plots.R | 20 ++++++++-------- 8 files changed, 51 insertions(+), 44 deletions(-)
Title: Extract, Analyze and Visualize Mutational Signatures for Genomic
Variations
Description: Genomic alterations including single nucleotide
substitution, copy number alteration, etc. are the major force for
cancer initialization and development. Due to the specificity of
molecular lesions caused by genomic alterations, we can generate
characteristic alteration spectra, called 'signature' (Wang, Shixiang,
et al. (2020) <DOI:10.1101/2020.04.27.20082404> & Alexandrov, Ludmil
B., et al. (2020) <DOI:10.1038/s41586-020-1943-3> & Macintyre, Geoff,
et al. (2018) <DOI:10.1038/s41588-018-0179-8>). This package helps
users to extract, analyze and visualize signatures from genomic
alteration records, thus providing new insight into cancer study.
Author: Shixiang Wang [aut, cre] (<https://orcid.org/0000-0001-9855-7357>),
Ziyu Tao [aut] (<https://orcid.org/0000-0003-3272-1227>),
Huimin Li [aut] (<https://orcid.org/0000-0003-1683-9057>),
Tao Wu [aut] (<https://orcid.org/0000-0002-8999-9628>),
Xue-Song Liu [aut, ctb] (<https://orcid.org/0000-0002-7736-0077>),
Geoffrey Macintyre [ctb],
Anand Mayakonda [ctb]
Maintainer: Shixiang Wang <w_shixiang@163.com>
Diff between sigminer versions 1.1.0 dated 2020-11-11 and 1.2.1 dated 2021-01-08
DESCRIPTION | 47 ++-- MD5 | 161 ++++++++------ NAMESPACE | 12 + NEWS.md | 40 +++ R/CN-mutex-classification-methed.R | 42 ++- R/best_practice.R |only R/best_practice_helper.R |only R/cosine.R | 2 R/data.R | 20 + R/get.R | 2 R/get_bayesian_result.R | 19 - R/get_groups.R | 16 + R/get_reconstructed_similarity.R |only R/get_sig_similarity.R | 42 ++- R/globalVariables.R | 8 R/group_enrichment.R | 38 +-- R/handle_hyper_mutation.R | 23 ++ R/helper_fit_cn_components.R | 5 R/helper_join_segments.R | 18 - R/helper_scale_nmf_matrix.R | 2 R/read_copynumber.R | 21 + R/read_vcf.R | 78 +++++++ R/same_size_clustering.R | 19 - R/scoring.R | 2 R/show_cor.R | 20 + R/show_cosmic_signature.R | 13 - R/show_group_distribution.R | 4 R/show_group_enrichment.R | 76 +++++-- R/show_sig_bootstrap.R | 3 R/show_sig_feature_corrplot.R | 12 - R/show_sig_number_survey.R | 16 + R/show_sig_number_survey2.R | 2 R/show_sig_profile.R | 30 +- R/show_sig_profile_loop.R | 12 - R/sig_auto_extract.R | 30 -- R/sig_estimate.R | 17 - R/sig_extract.R | 85 +++---- R/sig_fit.R | 105 ++++----- R/sig_fit_bootstrap.R | 31 +- R/sig_fit_bootstrap_batch.R | 11 - R/sig_tally.R | 18 + R/signature_obj_operation.R | 2 R/sigprofiler.R | 50 ---- R/simulation.R | 16 + R/utils.R | 37 ++- R/utils_mem.R |only README.md | 154 +++++++------- build/partial.rdb |only build/vignette.rds |binary data/simulated_catalogs.rda |only inst/doc/sigminer.R |only inst/doc/sigminer.Rmd | 101 ++++++++- inst/doc/sigminer.html | 336 +++++++++++++++++-------------- inst/py |only man/CN.features.Rd | 4 man/bp.Rd |only man/cosine.Rd | 2 man/figures/README-unnamed-chunk-1-1.png |binary man/figures/README-unnamed-chunk-2-1.png |binary man/figures/README-unnamed-chunk-3-1.png |binary man/figures/README-unnamed-chunk-4-1.png |binary man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-8-1.png |binary man/get_groups.Rd | 12 - man/get_sig_rec_similarity.Rd |only man/group_enrichment.Rd | 13 - man/read_copynumber.Rd | 2 man/read_vcf.Rd | 4 man/read_xena_variants.Rd |only man/same_size_clustering.Rd | 7 man/scoring.Rd | 2 man/show_cor.Rd | 5 man/show_group_distribution.Rd | 4 man/show_group_enrichment.Rd | 8 man/show_sig_bootstrap.Rd | 3 man/show_sig_number_survey.Rd | 5 man/show_sig_number_survey2.Rd | 2 man/sig_estimate.Rd | 8 man/sig_extract.Rd | 18 + man/sig_fit.Rd | 17 + man/sig_fit_bootstrap.Rd | 7 man/sig_fit_bootstrap_batch.Rd | 3 man/sig_operation.Rd | 3 man/sig_tally.Rd | 2 man/simulated_catalogs.Rd |only man/simulation.Rd | 4 vignettes/e1.rds |only vignettes/sigminer.Rmd | 101 ++++++++- 88 files changed, 1277 insertions(+), 757 deletions(-)
Title: Radiomics Image Analysis Toolbox for Medial Images
Description: Radiomics image analysis toolbox for 2D and 3D radiological images. RIA supports DICOM, NIfTI and
nrrd file formats. RIA calculates first-order, gray level co-occurrence matrix,
gray level run length matrix and geometry-based statistics. Almost all calculations are done
using vectorized formulas to optimize run speeds. Calculation of several thousands of parameters
only takes minutes on a single core of a conventional PC.
Author: Marton Kolossvary [aut, cre]
Maintainer: Marton Kolossvary <marton.kolossvary@gmail.com>
Diff between RIA versions 1.4.2 dated 2019-04-09 and 1.4.3 dated 2021-01-08
DESCRIPTION | 10 MD5 | 92 +++---- R/DICOM_codes.R | 4 R/NRS.R | 4 R/Non_NRS.R | 8 R/discretize.R | 4 R/first_order.R | 4 R/geometry.R | 4 R/geometry_plus.R | 2 R/glcm.R | 6 R/glcm_all.R | 6 R/glcm_stat.R | 4 R/glcm_stat_all.R | 4 R/glrlm.R | 6 R/glrlm_all.R | 5 R/glrlm_stat.R | 4 R/glrlm_stat_all.R | 4 R/load_dicom.R | 582 +++++++++++++++++++++++++------------------------- R/load_nifti.R | 514 ++++++++++++++++++++++---------------------- R/load_nrrd.R | 510 ++++++++++++++++++++++--------------------- R/radiomics_all.R | 25 +- R/save_RIA.R | 4 README.md | 38 ++- build/vignette.rds |binary inst/doc/RIA.R | 2 inst/doc/RIA.Rmd | 12 - inst/doc/RIA.html | 16 - man/DICOM_codes.Rd | 4 man/NRS.Rd | 4 man/Non_NRS.Rd | 8 man/discretize.Rd | 4 man/first_order.Rd | 4 man/geometry.Rd | 4 man/glcm.Rd | 6 man/glcm_all.Rd | 6 man/glcm_stat.Rd | 4 man/glcm_stat_all.Rd | 4 man/glrlm.Rd | 6 man/glrlm_all.Rd | 5 man/glrlm_stat.Rd | 4 man/glrlm_stat_all.Rd | 4 man/load_dicom.Rd | 11 man/load_nifti.Rd | 11 man/load_nrrd.Rd | 11 man/radiomics_all.Rd | 18 - man/save_RIA.Rd | 4 vignettes/RIA.Rmd | 12 - 47 files changed, 1040 insertions(+), 968 deletions(-)
Title: Integrative Survival Modeling
Description: Contains implementations of
integrative survival analysis routines, including
regular Cox cure rate model proposed by
Kuk and Chen (1992) <doi:10.1093/biomet/79.3.531>
via an EM algorithm proposed by
Sy and Taylor (2000) <doi:10.1111/j.0006-341X.2000.00227.x>,
regularized Cox cure rate model with elastic net penalty following
Masud et al. (2018) <doi:10.1177/0962280216677748>, and
Zou and Hastie (2005) <doi:10.1111/j.1467-9868.2005.00503.x>, and
weighted concordance index for cure models proposed by
Asano and Hirakawa (2017) <doi:10.1080/10543406.2017.1293082>.
Author: Wenjie Wang [aut, cre] (<https://orcid.org/0000-0003-0363-3180>),
Kun Chen [ctb] (<https://orcid.org/0000-0003-3579-5467>),
Jun Yan [ctb] (<https://orcid.org/0000-0003-4401-7296>)
Maintainer: Wenjie Wang <wang@wwenjie.org>
Diff between intsurv versions 0.2.1 dated 2019-12-17 and 0.2.2 dated 2021-01-08
intsurv-0.2.1/intsurv/inst/include/intsurv/splines.h |only intsurv-0.2.2/intsurv/DESCRIPTION | 17 intsurv-0.2.2/intsurv/MD5 | 104 +- intsurv-0.2.2/intsurv/NAMESPACE | 1 intsurv-0.2.2/intsurv/NEWS.md | 19 intsurv-0.2.2/intsurv/R/RcppExports.R | 57 - intsurv-0.2.2/intsurv/R/Survi.R | 2 intsurv-0.2.2/intsurv/R/assessment.R | 11 intsurv-0.2.2/intsurv/R/bootSe.R | 6 intsurv-0.2.2/intsurv/R/class.R | 2 intsurv-0.2.2/intsurv/R/coef.R | 2 intsurv-0.2.2/intsurv/R/cox_cure.R | 167 ++-- intsurv-0.2.2/intsurv/R/cox_cure_net.R | 294 ++----- intsurv-0.2.2/intsurv/R/iCoxph.R | 25 intsurv-0.2.2/intsurv/R/intsurv.R | 20 intsurv-0.2.2/intsurv/R/misc.R | 2 intsurv-0.2.2/intsurv/R/prep_model.R | 19 intsurv-0.2.2/intsurv/R/print.R | 2 intsurv-0.2.2/intsurv/R/show.R | 2 intsurv-0.2.2/intsurv/R/simData4cure.R | 19 intsurv-0.2.2/intsurv/R/simData4iCoxph.R | 13 intsurv-0.2.2/intsurv/R/summary.R | 2 intsurv-0.2.2/intsurv/README.md | 33 intsurv-0.2.2/intsurv/inst/CITATION | 35 intsurv-0.2.2/intsurv/inst/examples/cox_cure.R | 17 intsurv-0.2.2/intsurv/inst/include/intsurv.h | 9 intsurv-0.2.2/intsurv/inst/include/intsurv/assessment.h | 2 intsurv-0.2.2/intsurv/inst/include/intsurv/coxph_cure.h | 255 +++++- intsurv-0.2.2/intsurv/inst/include/intsurv/coxph_cure_uncer.h | 377 ++++++---- intsurv-0.2.2/intsurv/inst/include/intsurv/coxph_reg.h | 74 + intsurv-0.2.2/intsurv/inst/include/intsurv/cross-validation.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/cv_coxph_cure.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/cv_coxph_cure_uncer.h |only intsurv-0.2.2/intsurv/inst/include/intsurv/logistic_reg.h | 36 intsurv-0.2.2/intsurv/inst/include/intsurv/nonparametric.h | 2 intsurv-0.2.2/intsurv/inst/include/intsurv/utils.h | 122 +++ intsurv-0.2.2/intsurv/inst/tinytest/test-cox_cure.R | 3 intsurv-0.2.2/intsurv/man/bootSe.Rd | 9 intsurv-0.2.2/intsurv/man/cox_cure.Rd | 158 ++-- intsurv-0.2.2/intsurv/man/cox_cure_net.Rd | 285 ++++--- intsurv-0.2.2/intsurv/man/iCoxph.Rd | 20 intsurv-0.2.2/intsurv/man/iCoxph.control.Rd | 13 intsurv-0.2.2/intsurv/man/iCoxph.start.Rd | 10 intsurv-0.2.2/intsurv/man/intsurv-package.Rd | 16 intsurv-0.2.2/intsurv/man/simData4cure.Rd | 31 intsurv-0.2.2/intsurv/man/simData4iCoxph.Rd | 30 intsurv-0.2.2/intsurv/src/RcppExports.cpp | 145 +-- intsurv-0.2.2/intsurv/src/assessment_export.cpp | 2 intsurv-0.2.2/intsurv/src/coxph_cure_export.cpp | 89 ++ intsurv-0.2.2/intsurv/src/coxph_cure_uncer_export.cpp | 103 +- intsurv-0.2.2/intsurv/src/coxph_reg_export.cpp | 2 intsurv-0.2.2/intsurv/src/logistic_reg_export.cpp | 22 intsurv-0.2.2/intsurv/src/nonparametric_export.cpp | 2 intsurv-0.2.2/intsurv/src/utils_export.cpp | 2 intsurv-0.2.2/intsurv/tests/tinytest.R | 2 55 files changed, 1678 insertions(+), 1014 deletions(-)
Title: Hexagonal Binning Routines
Description: Binning and plotting functions for hexagonal bins.
Author: Dan Carr <dcarr@voxel.galaxy.gmu.edu>, ported by Nicholas
Lewin-Koh and Martin Maechler <maechler@stat.math.ethz.ch>,
contains copies of lattice functions written by Deepayan Sarkar
<deepayan.sarkar@r-project.org>
Maintainer: Edzer Pebesma <edzer.pebesma@uni-muenster.de>
Diff between hexbin versions 1.28.1 dated 2020-02-03 and 1.28.2 dated 2021-01-08
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/hexPlotMA.R | 4 ++-- R/hexViewport.R | 4 ++-- build/vignette.rds |binary inst/doc/hexagon_binning.pdf |binary man/hexMA.loess.Rd | 13 +++++++++---- 7 files changed, 23 insertions(+), 18 deletions(-)
Title: Interface to Download Meteorological (and Hydrological) Datasets
Description: Automatize downloading of meteorological and hydrological data from publicly available repositories:
OGIMET (<http://ogimet.com/index.phtml.en>),
University of Wyoming - atmospheric vertical profiling data (<http://weather.uwyo.edu/upperair>),
Polish Institute of Meterology and Water Management - National Research Institute (<https://dane.imgw.pl>),
and National Oceanic & Atmospheric Administration (NOAA).
This package also allows for adding geographical coordinates for each observation.
Author: Bartosz Czernecki [aut, cre] (<https://orcid.org/0000-0001-6496-1386>),
Arkadiusz Głogowski [aut] (<https://orcid.org/0000-0002-7587-8892>),
Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>),
IMGW-PIB [ctb] (source of the data)
Maintainer: Bartosz Czernecki <nwp@amu.edu.pl>
Diff between climate versions 0.9.8 dated 2020-08-03 and 0.9.9 dated 2021-01-08
DESCRIPTION | 8 - MD5 | 90 ++++++------- NEWS.md | 6 R/hydro_imgw.R | 4 R/hydro_imgw_annual.R | 2 R/hydro_imgw_daily.R | 2 R/hydro_imgw_monthly.R | 2 R/hydro_metadata_imgw.R | 2 R/hydro_shortening_imgw.R | 2 R/imgw_hydro_abbrev.R | 2 R/imgw_hydro_stations.R | 2 R/imgw_meteo_abbrev.R | 2 R/imgw_meteo_stations.R | 2 R/meteo_imgw.R | 4 R/meteo_imgw_daily.R | 2 R/meteo_imgw_hourly.R | 2 R/meteo_imgw_monthly.R | 2 R/meteo_metadata_imgw.R | 2 R/meteo_shortening_imgw.R | 2 R/nearest_stations_ogimet.R | 37 +++-- R/ogimet_daily.R | 196 ++++++++++++++++-------------- R/onAttach.R | 3 README.md | 13 +- inst/doc/getstarted.R | 6 inst/doc/getstarted.Rmd | 8 - inst/doc/getstarted.html | 264 ++++++++++++++++++++--------------------- man/hydro_imgw.Rd | 4 man/hydro_imgw_annual.Rd | 2 man/hydro_imgw_daily.Rd | 2 man/hydro_imgw_monthly.Rd | 2 man/hydro_metadata_imgw.Rd | 2 man/hydro_shortening_imgw.Rd | 2 man/imgw_hydro_abbrev.Rd | 2 man/imgw_hydro_stations.Rd | 2 man/imgw_meteo_abbrev.Rd | 2 man/imgw_meteo_stations.Rd | 2 man/meteo_imgw.Rd | 4 man/meteo_imgw_daily.Rd | 2 man/meteo_imgw_hourly.Rd | 2 man/meteo_imgw_monthly.Rd | 2 man/meteo_metadata_imgw.Rd | 2 man/meteo_shortening_imgw.Rd | 2 man/nearest_stations_ogimet.Rd | 11 + man/ogimet_daily.Rd | 5 tests/testthat/Rplots.pdf |binary vignettes/getstarted.Rmd | 8 - 46 files changed, 387 insertions(+), 340 deletions(-)
Title: Bayesian Preference Learning with the Mallows Rank Model
Description: An implementation of the Bayesian version of the Mallows rank model
(Vitelli et al., Journal of Machine Learning Research, 2018 <https://jmlr.org/papers/v18/15-481.html>;
Crispino et al., Annals of Applied Statistics, 2019 <doi:10.1214/18-AOAS1203>). Both Cayley, footrule,
Hamming, Kendall, Spearman, and Ulam distances are supported in the models. The rank data to be
analyzed can be in the form of complete rankings, top-k rankings, partially missing rankings, as well
as consistent and inconsistent pairwise preferences. Several functions for plotting and studying the
posterior distributions of parameters are provided. The package also provides functions for estimating
the partition function (normalizing constant) of the Mallows rank model, both with the importance
sampling algorithm of Vitelli et al. and asymptotic approximation with the IPFP algorithm
(Mukherjee, Annals of Statistics, 2016 <doi:10.1214/15-AOS1389>).
Author: Oystein Sorensen [aut, cre] (<https://orcid.org/0000-0003-0724-3542>),
Valeria Vitelli [aut] (<https://orcid.org/0000-0002-6746-0453>),
Marta Crispino [aut],
Qinghua Liu [aut],
Cristina Mollica [aut],
Luca Tardella [aut]
Maintainer: Oystein Sorensen <oystein.sorensen.1985@gmail.com>
Diff between BayesMallows versions 0.5.0 dated 2020-08-28 and 1.0.0 dated 2021-01-08
DESCRIPTION | 37 ++++++- MD5 | 100 ++++++++++++-------- NAMESPACE | 4 NEWS.md | 8 + R/BayesMallows.R | 4 R/Lik_DB_MIX.R |only R/RcppExports.R | 46 +++++++-- R/compute_mallows.R | 105 +++++++++++++++------- R/estimate_partition_function.R | 15 ++- R/expected_dist.R |only R/misc_expected_dist.R |only R/misc_likelihood.R |only R/obs_freq.R |only R/rank_distance.R |only R/rank_freq_distr.R |only R/sample_mallows.R | 5 - R/sysdata.rda |binary build/partial.rdb |binary build/vignette.rds |binary inst/CITATION | 7 + inst/REFERENCES.bib | 17 ++- inst/doc/BayesMallows.pdf |binary inst/examples/Lik_DB_MIX_example.R |only inst/examples/compute_mallows_example.R | 14 ++ inst/examples/expected_dist_example.R |only inst/examples/obs_freq_example.R |only inst/examples/rank_distance_example.R |only inst/examples/rank_freq_distr_example.R |only man/BayesMallows.Rd | 4 man/compute_mallows.Rd | 91 +++++++++++++------ man/estimate_partition_function.Rd | 9 + man/expected_dist.Rd |only man/figures/README-unnamed-chunk-5-1.png |binary man/figures/README-unnamed-chunk-6-1.png |binary man/get_partition_function.Rd | 11 +- man/get_rank_distance.Rd | 7 - man/lik_db_mix.Rd |only man/log_expected_dist.Rd |only man/obs_freq.Rd |only man/rank_distance.Rd |only man/rank_freq_distr.Rd |only man/rmallows.Rd | 3 man/run_mcmc.Rd | 3 man/sample_mallows.Rd | 2 src/RcppExports.cpp | 63 +++++++++++-- src/distances.cpp | 31 +++--- src/distances.h | 5 - src/mixtures.cpp | 6 - src/mixtures.h | 4 src/parameterupdates.cpp | 15 +-- src/parameterupdates.h | 3 src/partitionfuns.cpp | 42 +++++++- src/rmallows.cpp | 4 src/run_mcmc.cpp | 14 +- tests/testthat/test-Lik_DB_MIX.R |only tests/testthat/test-rank_freq_distr.R |only tests/testthat/test_compute_mallows.R | 85 +++++++++++++++++ tests/testthat/test_distance_function.R | 30 ++++++ tests/testthat/test_estimate_partition_function.R |only tests/testthat/test_expected_dist.R |only tests/testthat/test_random_number_seed.R | 77 +++++++--------- tests/testthat/test_sample_mallows.R | 2 62 files changed, 653 insertions(+), 220 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-04 0.17.0
2019-09-29 0.16.2
2019-01-04 0.16.1
2018-07-10 0.16.0
2017-09-11 0.15.0
2017-05-31 0.14.1
2017-03-18 0.14.0
2016-10-21 0.13.1
2016-08-03 0.13.0
2016-06-27 0.12.1
2016-06-26 0.12.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2021-01-06 0.6.0
2019-02-01 0.5.0
2017-10-13 0.4.2
2017-09-15 0.4.0
2016-10-25 0.3.0
2016-05-03 0.1.7
2016-03-04 0.1.6
2015-08-24 0.1.4
2015-05-16 0.1.0
Title: GUI Tools for Interactive Image Processing with 'magick'
Description: Enables us to use the functions of the package 'magick' interactively.
Author: Shota Ochi [aut, cre]
Maintainer: Shota Ochi <shotaochi1990@gmail.com>
Diff between magickGUI versions 1.2.0 dated 2020-06-23 and 1.2.2 dated 2021-01-08
DESCRIPTION | 6 - MD5 | 102 +++++++++++++------------- NAMESPACE | 2 NEWS.md | 10 ++ R/interactive_annotate.R | 26 +++++- R/interactive_blur.R | 16 +++- R/interactive_canny.R | 13 ++- R/interactive_charcoal.R | 16 +++- R/interactive_composite.R | 31 ++++++- R/interactive_crop.R | 34 +++++++- R/interactive_despeckle.R | 13 ++- R/interactive_emboss.R | 16 +++- R/interactive_fill.R | 26 +++++- R/interactive_implode.R | 13 ++- R/interactive_modulate.R | 13 ++- R/interactive_oilpaint.R | 13 ++- R/interactive_quantize.R | 13 ++- R/interactive_reducenoise.R | 13 ++- R/interactive_threshold.R | 13 ++- R/misc.R | 2 man/interactive_annotate.Rd | 5 + man/interactive_blur.Rd | 5 + man/interactive_canny.Rd | 5 + man/interactive_charcoal.Rd | 5 + man/interactive_composite.Rd | 5 + man/interactive_crop.Rd | 4 - man/interactive_despeckle.Rd | 5 + man/interactive_emboss.Rd | 5 + man/interactive_fill.Rd | 5 + man/interactive_implode.Rd | 5 + man/interactive_modulate.Rd | 5 + man/interactive_oilpaint.Rd | 5 + man/interactive_quantize.Rd | 5 + man/interactive_reducenoise.Rd | 5 + man/interactive_threshold.Rd | 5 + tests/testthat/setup-global_variable.R | 3 tests/testthat/teardown-global_variable.R | 2 tests/testthat/test_interactive_annotate.R | 2 tests/testthat/test_interactive_blur.R | 2 tests/testthat/test_interactive_canny.R | 2 tests/testthat/test_interactive_charcoal.R | 2 tests/testthat/test_interactive_composite.R | 2 tests/testthat/test_interactive_crop.R | 2 tests/testthat/test_interactive_despeckle.R | 2 tests/testthat/test_interactive_emboss.R | 2 tests/testthat/test_interactive_fill.R | 2 tests/testthat/test_interactive_implode.R | 2 tests/testthat/test_interactive_modulate.R | 2 tests/testthat/test_interactive_oilpaint.R | 2 tests/testthat/test_interactive_quantize.R | 2 tests/testthat/test_interactive_reducenoise.R | 2 tests/testthat/test_interactive_threshold.R | 2 52 files changed, 387 insertions(+), 113 deletions(-)
Title: Solving Differential Equations (ODEs, SDEs, DDEs, DAEs)
Description: An interface to 'DifferentialEquations.jl' <https://diffeq.sciml.ai/dev/> from the R programming language.
It has unique high performance methods for solving ordinary differential equations (ODE), stochastic differential equations (SDE),
delay differential equations (DDE), differential-algebraic equations (DAE), and more. Much of the functionality,
including features like adaptive time stepping in SDEs, are unique and allow for multiple orders of magnitude speedup over more common methods.
'diffeqr' attaches an R interface onto the package, allowing seamless use of this tooling by R users.
Author: Christopher Rackauckas [aut, cre]
Maintainer: Christopher Rackauckas <me@chrisrackauckas.com>
Diff between diffeqr versions 1.0.0 dated 2020-08-26 and 1.1.0 dated 2021-01-08
DESCRIPTION | 6 MD5 | 26 - R/diffeqr.R | 11 README.md | 23 + inst/doc/dae.html | 509 ++++++++++++-------------------------- inst/doc/dde.html | 487 ++++++++++++------------------------ inst/doc/gpu.html | 689 ++++++++++++++++++++++------------------------------ inst/doc/ode.Rmd | 4 inst/doc/ode.html | 685 +++++++++++++++++++++------------------------------ inst/doc/sde.Rmd | 10 inst/doc/sde.html | 656 ++++++++++++++++++++----------------------------- man/diffeq_setup.Rd | 6 vignettes/ode.Rmd | 4 vignettes/sde.Rmd | 10 14 files changed, 1248 insertions(+), 1878 deletions(-)
Title: Sparse Three-Dimensional Arrays and Linear Algebra Utilities
Description: Defines sparse three-dimensional arrays
and supports standard operations on them.
The package also includes utility functions for
matrix calculations that are common in
statistics, such as quadratic forms.
Author: Adrian Baddeley [aut, cre, cph]
(<https://orcid.org/0000-0001-9499-8382>),
Rolf Turner [aut, cph] (<https://orcid.org/0000-0001-5521-5218>),
Ege Rubak [aut, cph] (<https://orcid.org/0000-0002-6675-533X>)
Maintainer: Adrian Baddeley <Adrian.Baddeley@curtin.edu.au>
Diff between spatstat.sparse versions 1.1-0 dated 2020-06-04 and 1.2-0 dated 2021-01-08
DESCRIPTION | 10 +++++----- MD5 | 12 ++++++------ NAMESPACE | 26 +++++++++++++------------- R/linalg.R | 22 +++++++++++----------- R/sparselinalg.R | 10 +++++----- inst/doc/packagesizes.txt | 11 +++++++++++ src/init.c | 1 + 7 files changed, 52 insertions(+), 40 deletions(-)
More information about spatstat.sparse at CRAN
Permanent link
Title: Normalized Stochasticity Ratio
Description: To estimate ecological stochasticity in community assembly. Understanding the community assembly mechanisms controlling biodiversity patterns is a central issue in ecology. Although it is generally accepted that both deterministic and stochastic processes play important roles in community assembly, quantifying their relative importance is challenging. The new index, normalized stochasticity ratio (NST), is to estimate ecological stochasticity, i.e. relative importance of stochastic processes, in community assembly. With functions in this package, NST can be calculated based on different similarity metrics and/or different null model algorithms, as well as some previous indexes, e.g. previous Stochasticity Ratio (ST), Standard Effect Size (SES), modified Raup-Crick metrics (RC). Functions for permutational test and bootstrapping analysis are also included. Previous ST is published by Zhou et al (2014) <doi:10.1073/pnas.1324044111>. NST is modified from ST by considering two alternative situations and normalizing the index to range from 0 to 1 (Ning et al 2019) <doi:10.1073/pnas.1904623116>. A modified version, MST, is a special case of NST, used in some recent or upcoming publications, e.g. Liang et al (2020) <doi:10.1016/j.soilbio.2020.108023>. SES is calculated as described in Kraft et al (2011) <doi:10.1126/science.1208584>. RC is calculated as reported by Chase et al (2011) <doi:10.1890/es10-00117.1> and Stegen et al (2013) <doi:10.1038/ismej.2013.93>. Version 3 added NST based on phylogenetic beta diversity, used by Ning et al (2020) <doi:10.1038/s41467-020-18560-z>.
Author: Daliang Ning
Maintainer: Daliang Ning <ningdaliang@ou.edu>
Diff between NST versions 3.0.3 dated 2020-09-16 and 3.0.6 dated 2021-01-08
DESCRIPTION | 11 ++-- MD5 | 16 +++--- R/nst.boot.r | 129 ++++++++++++++++++++++++++++++++++++++++++----------- R/nst.panova.r | 25 ++++++---- man/NST-package.Rd | 9 ++- man/nst.boot.Rd | 13 ++--- man/nst.panova.Rd | 5 +- man/pNST.Rd | 8 +-- man/tNST.Rd | 6 +- 9 files changed, 154 insertions(+), 68 deletions(-)
Title: A Graphical EDA Tool
Description: An automated graphical exploratory data analysis (EDA) tool that introduces:
a.) wideplot() graphics for exploring the structure of a dataset through a grid of variables
and graphic types.
b.) longplot() graphics, which present the entire catalog of available graphics for representing
a particular variable using a grid of graphic types and variations on these types.
c.) plotup() function, which presents a particular graphic for a specific variable of a dataset.
The plotup() function also makes it possible to obtain the code used to generate the graphic,
meaning that the user can adjust its properties as needed.
Author: Pere Millán-Martínez [aut, cre],
Ramon Oller Piqué [ctb]
Maintainer: Pere Millán-Martínez <info@sciencegraph.org>
Diff between brinton versions 0.2.1 dated 2020-08-31 and 0.2.4 dated 2021-01-08
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