Title: Clinical Trial Designs in 'RStan'
Description: A showcase of Bayesian clinical trial designs, implemented in
'RStan' and R, including the Continual Reassessment Method (CRM) and EffTox.
Given the emphasis on flexibility in Bayesian analysis,
the implementations in a common language and style may serve as a cookbook
to encourage the use of Bayesian methods in trials. Compiled 'RStan' models
are installed, alongside helper classes and functions to work with models.
There is a preponderance of early phase trial designs because this is where
Bayesian methods are used most. If there is a published Bayesian design you
want implemented in 'Stan', get in touch.
Author: Kristian Brock [aut, cre] (<https://orcid.org/0000-0002-3921-0166>),
Trustees of Columbia University [cph]
Maintainer: Kristian Brock <kristian.brock@gmail.com>
Diff between trialr versions 0.1.0 dated 2019-04-21 and 0.1.1 dated 2019-05-24
trialr-0.1.0/trialr/R/dosefinding.R |only trialr-0.1.0/trialr/R/hierarchical.R |only trialr-0.1.0/trialr/R/peps2.R |only trialr-0.1.0/trialr/tests/testthat/test_dosefinding.R |only trialr-0.1.1/trialr/DESCRIPTION | 21 trialr-0.1.1/trialr/MD5 | 187 trialr-0.1.1/trialr/NAMESPACE | 38 trialr-0.1.1/trialr/NEWS.md | 5 trialr-0.1.1/trialr/R/CRM.R | 421 trialr-0.1.1/trialr/R/EffTox.R | 1081 trialr-0.1.1/trialr/R/careful_escalation.R |only trialr-0.1.1/trialr/R/crm_dtps.R |only trialr-0.1.1/trialr/R/crm_fit.R |only trialr-0.1.1/trialr/R/crm_params.R |only trialr-0.1.1/trialr/R/crm_path_analysis.R |only trialr-0.1.1/trialr/R/crm_prior_beliefs.R |only trialr-0.1.1/trialr/R/crm_process.R |only trialr-0.1.1/trialr/R/df_parse_outcomes.R |only trialr-0.1.1/trialr/R/dose_finding_fit.R |only trialr-0.1.1/trialr/R/dose_finding_path_node.R |only trialr-0.1.1/trialr/R/dose_finding_paths.R |only trialr-0.1.1/trialr/R/efftox_contour_plot.R |only trialr-0.1.1/trialr/R/efftox_dtps.R |only trialr-0.1.1/trialr/R/efftox_dtps_to_dataframe.R |only trialr-0.1.1/trialr/R/efftox_fit.R |only trialr-0.1.1/trialr/R/efftox_parameters_demo.R |only trialr-0.1.1/trialr/R/efftox_params.R |only trialr-0.1.1/trialr/R/efftox_parse_outcomes.R |only trialr-0.1.1/trialr/R/efftox_path_analysis.R |only trialr-0.1.1/trialr/R/efftox_process.R |only trialr-0.1.1/trialr/R/efftox_simulate.R |only trialr-0.1.1/trialr/R/efftox_solve_p.R |only trialr-0.1.1/trialr/R/efftox_superiority.R |only trialr-0.1.1/trialr/R/efftox_utility.R |only trialr-0.1.1/trialr/R/efftox_utility_density_plot.R |only trialr-0.1.1/trialr/R/misc.R |only trialr-0.1.1/trialr/R/parse_dose_finding_outcomes.R |only trialr-0.1.1/trialr/R/parse_eff_tox_dose_finding_outcomes.R |only trialr-0.1.1/trialr/R/peps2_get_data.R |only trialr-0.1.1/trialr/R/peps2_process.R |only trialr-0.1.1/trialr/R/prob_tox_exceeds.R |only trialr-0.1.1/trialr/R/spread_paths.R |only trialr-0.1.1/trialr/R/stan_crm.R |only trialr-0.1.1/trialr/R/stan_efftox.R |only trialr-0.1.1/trialr/R/stan_efftox_demo.R |only trialr-0.1.1/trialr/R/stan_hierarchical_response_thall.R |only trialr-0.1.1/trialr/R/stan_peps2.R |only trialr-0.1.1/trialr/README.md | 397 trialr-0.1.1/trialr/build/vignette.rds |binary trialr-0.1.1/trialr/inst/doc/BEBOP.html | 8 trialr-0.1.1/trialr/inst/doc/CRM-pathways.R |only trialr-0.1.1/trialr/inst/doc/CRM-pathways.Rmd |only trialr-0.1.1/trialr/inst/doc/CRM-pathways.html |only trialr-0.1.1/trialr/inst/doc/CRM-visualisation.R | 69 trialr-0.1.1/trialr/inst/doc/CRM-visualisation.Rmd | 75 trialr-0.1.1/trialr/inst/doc/CRM-visualisation.html | 131 trialr-0.1.1/trialr/inst/doc/CRM.Rmd | 4 trialr-0.1.1/trialr/inst/doc/CRM.html | 70 trialr-0.1.1/trialr/inst/doc/EffTox.html | 38 trialr-0.1.1/trialr/inst/doc/HierarchicalBayesianResponse.html | 266 trialr-0.1.1/trialr/inst/doc/LevyCaseStudy.R |only trialr-0.1.1/trialr/inst/doc/LevyCaseStudy.Rmd |only trialr-0.1.1/trialr/inst/doc/LevyCaseStudy.html |only trialr-0.1.1/trialr/inst/doc/TITE-CRM.Rmd | 4 trialr-0.1.1/trialr/inst/doc/TITE-CRM.html | 25 trialr-0.1.1/trialr/man/as.mcmc.list.crm_fit.Rd |only trialr-0.1.1/trialr/man/as.mcmc.list.efftox_fit.Rd |only trialr-0.1.1/trialr/man/as_tibble.dose_finding_paths.Rd |only trialr-0.1.1/trialr/man/careful_escalation.Rd |only trialr-0.1.1/trialr/man/closest_to_target.Rd |only trialr-0.1.1/trialr/man/crm_codified_dose_logistic.Rd |only trialr-0.1.1/trialr/man/crm_dtps.Rd |only trialr-0.1.1/trialr/man/crm_fit-class.Rd | 29 trialr-0.1.1/trialr/man/crm_params-class.Rd | 45 trialr-0.1.1/trialr/man/crm_path_analysis.Rd |only trialr-0.1.1/trialr/man/crm_prior_beliefs.Rd |only trialr-0.1.1/trialr/man/crm_process.Rd | 4 trialr-0.1.1/trialr/man/df_parse_outcomes.Rd | 11 trialr-0.1.1/trialr/man/dose_finding_fit-class.Rd |only trialr-0.1.1/trialr/man/dose_finding_path_node-class.Rd |only trialr-0.1.1/trialr/man/efftox_contour_plot.Rd | 6 trialr-0.1.1/trialr/man/efftox_dtps.Rd | 146 trialr-0.1.1/trialr/man/efftox_dtps_to_dataframe.Rd |only trialr-0.1.1/trialr/man/efftox_fit-class.Rd | 47 trialr-0.1.1/trialr/man/efftox_parameters_demo.Rd | 2 trialr-0.1.1/trialr/man/efftox_params-class.Rd | 5 trialr-0.1.1/trialr/man/efftox_parse_outcomes.Rd | 2 trialr-0.1.1/trialr/man/efftox_path_analysis.Rd |only trialr-0.1.1/trialr/man/efftox_process.Rd | 2 trialr-0.1.1/trialr/man/efftox_simulate.Rd | 6 trialr-0.1.1/trialr/man/efftox_solve_p.Rd | 2 trialr-0.1.1/trialr/man/efftox_superiority.Rd | 2 trialr-0.1.1/trialr/man/efftox_utility.Rd | 2 trialr-0.1.1/trialr/man/efftox_utility_density_plot.Rd | 2 trialr-0.1.1/trialr/man/figures/README-unnamed-chunk-11-1.png |binary trialr-0.1.1/trialr/man/figures/README-unnamed-chunk-14-1.png |binary trialr-0.1.1/trialr/man/figures/README-unnamed-chunk-6-1.png |binary trialr-0.1.1/trialr/man/parse_dose_finding_outcomes.Rd | 2 trialr-0.1.1/trialr/man/parse_eff_tox_dose_finding_outcomes.Rd |only trialr-0.1.1/trialr/man/peps2_get_data.Rd | 2 trialr-0.1.1/trialr/man/peps2_process.Rd | 2 trialr-0.1.1/trialr/man/prob_tox_exceeds.Rd |only trialr-0.1.1/trialr/man/spread_paths.Rd |only trialr-0.1.1/trialr/man/stan_crm.Rd | 72 trialr-0.1.1/trialr/man/stan_efftox.Rd | 11 trialr-0.1.1/trialr/man/stan_efftox_demo.Rd | 2 trialr-0.1.1/trialr/man/stan_hierarchical_response_thall.Rd | 6 trialr-0.1.1/trialr/man/stan_peps2.Rd | 2 trialr-0.1.1/trialr/man/summary.crm_fit.Rd | 3 trialr-0.1.1/trialr/tests/testthat/test_careful_escalation.R |only trialr-0.1.1/trialr/tests/testthat/test_crm_codified_dose_logistic.R |only trialr-0.1.1/trialr/tests/testthat/test_crm_dtps.R |only trialr-0.1.1/trialr/tests/testthat/test_df_parse_outcomes.R |only trialr-0.1.1/trialr/tests/testthat/test_efftox.R | 3 trialr-0.1.1/trialr/tests/testthat/test_efftox_dtps.R |only trialr-0.1.1/trialr/tests/testthat/test_efftox_dtps_to_dataframe.R |only trialr-0.1.1/trialr/tests/testthat/test_efftox_parse_outcomes.R | 32 trialr-0.1.1/trialr/tests/testthat/test_hierarchical.R | 10 trialr-0.1.1/trialr/tests/testthat/test_misc.R |only trialr-0.1.1/trialr/tests/testthat/test_parse_dose_finding_outcomes.R |only trialr-0.1.1/trialr/tests/testthat/test_parse_eff_tox_dose_finding_outcomes.R |only trialr-0.1.1/trialr/tests/testthat/test_spread_paths.R |only trialr-0.1.1/trialr/tests/testthat/test_stan_crm.R | 153 trialr-0.1.1/trialr/tests/testthat/test_stan_efftox.R | 36 trialr-0.1.1/trialr/vignettes/CRM-pathways.Rmd |only trialr-0.1.1/trialr/vignettes/CRM-visualisation.Rmd | 75 trialr-0.1.1/trialr/vignettes/CRM.Rmd | 4 trialr-0.1.1/trialr/vignettes/EffTox_cache/html/__packages | 8 trialr-0.1.1/trialr/vignettes/EffTox_cache/html/run_sims_f82b60090eba4ebe42c302621d520c5f.RData |binary trialr-0.1.1/trialr/vignettes/LevyCaseStudy.Rmd |only trialr-0.1.1/trialr/vignettes/TITE-CRM.Rmd | 4 trialr-0.1.1/trialr/vignettes/library.bib |15093 +++++----- 132 files changed, 9222 insertions(+), 9451 deletions(-)
Title: A Collection of Efficient and Extremely Fast R Functions
Description: A collection of fast (utility) functions for data analysis. Column- and row- wise means, medians, variances, minimums, maximums, many t, F and G-square tests, many regressions (normal, logistic, Poisson), are some of the many fast functions. Reference: Tsagris M, Papadakis M. (2018). Taking R to its limits: 70+ tips. PeerJ Preprints 6:e26605v1 <doi:10.7287/peerj.preprints.26605v1>.
Author: Manos Papadakis, Michail Tsagris, Marios Dimitriadis, Stefanos Fafalios, Ioannis Tsamardinos, Matteo Fasiolo, Giorgos Borboudakis, John Burkardt, Changliang Zou, Kleanthi Lakiotaki and Christina Chatzipantsiou.
Maintainer: Manos Papadakis <rfastofficial@gmail.com>
Diff between Rfast versions 1.9.3 dated 2019-03-04 and 1.9.4 dated 2019-05-24
Rfast-1.9.3/Rfast/R/AddToNamespace.R |only Rfast-1.9.3/Rfast/R/Choose.R |only Rfast-1.9.3/Rfast/R/Diag.fill.R |only Rfast-1.9.3/Rfast/R/Diag.matrix.R |only Rfast-1.9.3/Rfast/R/Digamma.R |only Rfast-1.9.3/Rfast/R/Hash.key.multi.R |only Rfast-1.9.3/Rfast/R/Lchoose.R |only Rfast-1.9.3/Rfast/R/Lgamma.R |only Rfast-1.9.3/Rfast/R/Pmax.R |only Rfast-1.9.3/Rfast/R/Pmin_Pmax.R |only Rfast-1.9.3/Rfast/R/RemoveFromNamespace.R |only Rfast-1.9.3/Rfast/R/Sort.int.R |only Rfast-1.9.3/Rfast/R/Table.sign.R |only Rfast-1.9.3/Rfast/R/Trigamma.R |only Rfast-1.9.3/Rfast/R/XopY.sum.R |only Rfast-1.9.3/Rfast/R/as.Rfast.function.R |only Rfast-1.9.3/Rfast/R/bincomb.R |only Rfast-1.9.3/Rfast/R/checkAliases.R |only Rfast-1.9.3/Rfast/R/checkExamples.R |only Rfast-1.9.3/Rfast/R/checkNamespace.R |only Rfast-1.9.3/Rfast/R/checkTF.R |only Rfast-1.9.3/Rfast/R/checkUsage.R |only Rfast-1.9.3/Rfast/R/colAll.R |only Rfast-1.9.3/Rfast/R/colAny.R |only Rfast-1.9.3/Rfast/R/colCountValues.R |only Rfast-1.9.3/Rfast/R/colCumMaxs.R |only Rfast-1.9.3/Rfast/R/colCumMins.R |only Rfast-1.9.3/Rfast/R/colCumProds.R |only Rfast-1.9.3/Rfast/R/colCumSums.R |only Rfast-1.9.3/Rfast/R/colFalse.R |only Rfast-1.9.3/Rfast/R/colMads.R |only Rfast-1.9.3/Rfast/R/colMaxs.R |only Rfast-1.9.3/Rfast/R/colMedians.R |only Rfast-1.9.3/Rfast/R/colMins.R |only Rfast-1.9.3/Rfast/R/colMinsMaxs.R |only Rfast-1.9.3/Rfast/R/colOrder.R |only Rfast-1.9.3/Rfast/R/colPmax.R |only Rfast-1.9.3/Rfast/R/colPmin.R |only Rfast-1.9.3/Rfast/R/colRanks.R |only Rfast-1.9.3/Rfast/R/colShuffle.R |only Rfast-1.9.3/Rfast/R/colSort.R |only Rfast-1.9.3/Rfast/R/colTabulate.R |only Rfast-1.9.3/Rfast/R/colTrue.R |only Rfast-1.9.3/Rfast/R/colTrueFalse.R |only Rfast-1.9.3/Rfast/R/colVars.R |only Rfast-1.9.3/Rfast/R/colnth.R |only Rfast-1.9.3/Rfast/R/colprods.R |only Rfast-1.9.3/Rfast/R/columns.R |only Rfast-1.9.3/Rfast/R/comb_n.R |only Rfast-1.9.3/Rfast/R/freq.max.R |only Rfast-1.9.3/Rfast/R/freq.min.R |only Rfast-1.9.3/Rfast/R/g2Test.R |only Rfast-1.9.3/Rfast/R/g2Test_perm.R |only Rfast-1.9.3/Rfast/R/g2Test_univariate.R |only Rfast-1.9.3/Rfast/R/g2Test_univariate_perm.R |only Rfast-1.9.3/Rfast/R/g2tests.R |only Rfast-1.9.3/Rfast/R/g2tests_perm.R |only Rfast-1.9.3/Rfast/R/hash.find.R |only Rfast-1.9.3/Rfast/R/hash.list.R |only Rfast-1.9.3/Rfast/R/hash2list.R |only Rfast-1.9.3/Rfast/R/is.symmetric.R |only Rfast-1.9.3/Rfast/R/is_element.R |only Rfast-1.9.3/Rfast/R/is_integer.R |only Rfast-1.9.3/Rfast/R/lower_tri.R |only Rfast-1.9.3/Rfast/R/lower_tri.assign.R |only Rfast-1.9.3/Rfast/R/mat.mat.R |only Rfast-1.9.3/Rfast/R/mat.mult.R |only Rfast-1.9.3/Rfast/R/med.R |only Rfast-1.9.3/Rfast/R/permutation.R |only Rfast-1.9.3/Rfast/R/permutation.next.R |only Rfast-1.9.3/Rfast/R/permutation.prev.R |only Rfast-1.9.3/Rfast/R/read.directory.R |only Rfast-1.9.3/Rfast/R/read.examples.R |only Rfast-1.9.3/Rfast/R/rep_col.R |only Rfast-1.9.3/Rfast/R/rep_row.R |only Rfast-1.9.3/Rfast/R/rowAll.R |only Rfast-1.9.3/Rfast/R/rowAny.R |only 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Rfast-1.9.4/Rfast/R/Tabulate.R |only Rfast-1.9.4/Rfast/R/Var.R | 26 Rfast-1.9.4/Rfast/R/acg.mle.R | 1 Rfast-1.9.4/Rfast/R/all_equals.R | 1 Rfast-1.9.4/Rfast/R/allbetas.R | 7 Rfast-1.9.4/Rfast/R/allttests.R | 1 Rfast-1.9.4/Rfast/R/ancova1.R | 7 Rfast-1.9.4/Rfast/R/ancovas.R | 5 Rfast-1.9.4/Rfast/R/anova1.R | 3 Rfast-1.9.4/Rfast/R/anova_propreg.R | 1 Rfast-1.9.4/Rfast/R/anova_qpois.reg.R | 1 Rfast-1.9.4/Rfast/R/anova_quasipois.reg.R | 1 Rfast-1.9.4/Rfast/R/anovas.R | 1 Rfast-1.9.4/Rfast/R/apply.condition.R | 3 Rfast-1.9.4/Rfast/R/ar1.R | 1 Rfast-1.9.4/Rfast/R/as_integer.R | 2 Rfast-1.9.4/Rfast/R/auc.R | 3 Rfast-1.9.4/Rfast/R/bc.R | 1 Rfast-1.9.4/Rfast/R/bcdcor.R | 3 Rfast-1.9.4/Rfast/R/beta.mle.R | 1 Rfast-1.9.4/Rfast/R/betabinom.mle.R | 1 Rfast-1.9.4/Rfast/R/betageom.mle.R | 1 Rfast-1.9.4/Rfast/R/betaprime.mle.R | 1 Rfast-1.9.4/Rfast/R/bic.corfsreg.R | 18 Rfast-1.9.4/Rfast/R/bic.fs.reg.R | 1 Rfast-1.9.4/Rfast/R/binary_search.R | 3 Rfast-1.9.4/Rfast/R/binom.mle.R | 1 Rfast-1.9.4/Rfast/R/block.anova.R | 5 Rfast-1.9.4/Rfast/R/block.anovas.R | 1 Rfast-1.9.4/Rfast/R/boot.ttest2.R | 1 Rfast-1.9.4/Rfast/R/borel.mle.R | 1 Rfast-1.9.4/Rfast/R/bs.reg.R | 2 Rfast-1.9.4/Rfast/R/btmprobs.R | 1 Rfast-1.9.4/Rfast/R/cat.goftests.R | 2 Rfast-1.9.4/Rfast/R/cauchy.mle.R | 1 Rfast-1.9.4/Rfast/R/check_data.R | 1 Rfast-1.9.4/Rfast/R/chi2Test.R | 2 Rfast-1.9.4/Rfast/R/chi2Test_univariate.R | 2 Rfast-1.9.4/Rfast/R/chi2tests.R | 2 Rfast-1.9.4/Rfast/R/chisq.mle.R | 1 Rfast-1.9.4/Rfast/R/cholesky.R | 2 Rfast-1.9.4/Rfast/R/circlin.cor.R | 1 Rfast-1.9.4/Rfast/R/col.coxpoisrat.R | 1 Rfast-1.9.4/Rfast/R/col.yule.R | 1 Rfast-1.9.4/Rfast/R/colanovas.R | 1 Rfast-1.9.4/Rfast/R/colar1.R | 1 Rfast-1.9.4/Rfast/R/colaucs.R | 2 Rfast-1.9.4/Rfast/R/colcvs.R | 1 Rfast-1.9.4/Rfast/R/coldiffs.R | 2 Rfast-1.9.4/Rfast/R/colexp2.mle.R | 1 Rfast-1.9.4/Rfast/R/colexpmle.R | 1 Rfast-1.9.4/Rfast/R/colgammamle.R | 1 Rfast-1.9.4/Rfast/R/colgeom.mle.R | 1 Rfast-1.9.4/Rfast/R/colhameans.R | 1 Rfast-1.9.4/Rfast/R/colinvgauss.mle.R | 1 Rfast-1.9.4/Rfast/R/colkurtosis.R | 1 Rfast-1.9.4/Rfast/R/collaplace.mle.R | 1 Rfast-1.9.4/Rfast/R/collindley.mle.R | 1 Rfast-1.9.4/Rfast/R/colmaxboltz.mle.R | 2 Rfast-1.9.4/Rfast/R/colmeans.R | 2 Rfast-1.9.4/Rfast/R/colnormal.mle.R | 1 Rfast-1.9.4/Rfast/R/colnormlog.mle.R | 2 Rfast-1.9.4/Rfast/R/colpareto.mle.R | 1 Rfast-1.9.4/Rfast/R/colpois.tests.R | 1 Rfast-1.9.4/Rfast/R/colpoisdisp.tests.R | 1 Rfast-1.9.4/Rfast/R/colpoisson.anovas.R | 1 Rfast-1.9.4/Rfast/R/colpoisson.mle.R | 1 Rfast-1.9.4/Rfast/R/colquasipoisson.anovas.R | 6 Rfast-1.9.4/Rfast/R/colrange.R | 3 Rfast-1.9.4/Rfast/R/colrayleigh.mle.R | 1 Rfast-1.9.4/Rfast/R/colrint.regbx.R | 1 Rfast-1.9.4/Rfast/R/colrow.value.R | 2 Rfast-1.9.4/Rfast/R/colskewness.R | 11 Rfast-1.9.4/Rfast/R/colsums.R | 2 Rfast-1.9.4/Rfast/R/colvarcomps.mle.R | 1 Rfast-1.9.4/Rfast/R/colvarcomps.mom.R | 1 Rfast-1.9.4/Rfast/R/colvm.mle.R | 1 Rfast-1.9.4/Rfast/R/colwatsons.R | 3 Rfast-1.9.4/Rfast/R/colweibull.mle.R | 1 Rfast-1.9.4/Rfast/R/cor.fbed.R | 5 Rfast-1.9.4/Rfast/R/cor.fsreg.R | 13 Rfast-1.9.4/Rfast/R/cora.R | 1 Rfast-1.9.4/Rfast/R/corpairs.R | 1 Rfast-1.9.4/Rfast/R/correls.R | 1 Rfast-1.9.4/Rfast/R/count_value.R | 20 Rfast-1.9.4/Rfast/R/cova.R | 1 Rfast-1.9.4/Rfast/R/cox.poisrat.R | 1 Rfast-1.9.4/Rfast/R/cqtest.R | 5 Rfast-1.9.4/Rfast/R/cqtests.R | 1 Rfast-1.9.4/Rfast/R/ct.mle.R | 1 Rfast-1.9.4/Rfast/R/cumulative.R |only Rfast-1.9.4/Rfast/R/data.frame.to_matrix.R | 2 Rfast-1.9.4/Rfast/R/dcor.R | 2 Rfast-1.9.4/Rfast/R/dcor.ttest.R | 1 Rfast-1.9.4/Rfast/R/dcov.R | 2 Rfast-1.9.4/Rfast/R/design_matrix.R | 2 Rfast-1.9.4/Rfast/R/diri.nr2.R | 9 Rfast-1.9.4/Rfast/R/dirimultinom.mle.R | 1 Rfast-1.9.4/Rfast/R/dirknn.R | 1 Rfast-1.9.4/Rfast/R/dirknn.cv.R | 1 Rfast-1.9.4/Rfast/R/dista.R | 2 Rfast-1.9.4/Rfast/R/dmvnorm.R | 1 Rfast-1.9.4/Rfast/R/dmvt.R | 1 Rfast-1.9.4/Rfast/R/dvar.R | 2 Rfast-1.9.4/Rfast/R/eachcol.apply.R | 2 Rfast-1.9.4/Rfast/R/eachrow.R | 2 Rfast-1.9.4/Rfast/R/edist.R | 6 Rfast-1.9.4/Rfast/R/eel.test1.R | 1 Rfast-1.9.4/Rfast/R/eel.test2.R | 1 Rfast-1.9.4/Rfast/R/eigen.sym.R | 1 Rfast-1.9.4/Rfast/R/el.test1.R | 1 Rfast-1.9.4/Rfast/R/el.test2.R | 1 Rfast-1.9.4/Rfast/R/env.copy.R | 2 Rfast-1.9.4/Rfast/R/exact.ttest2.R | 1 Rfast-1.9.4/Rfast/R/exp2.mle.R | 1 Rfast-1.9.4/Rfast/R/expmle.R | 1 Rfast-1.9.4/Rfast/R/expregs.R | 1 Rfast-1.9.4/Rfast/R/fish.kent.R | 1 Rfast-1.9.4/Rfast/R/floyd.R | 2 Rfast-1.9.4/Rfast/R/foldnorm.mle.R | 1 Rfast-1.9.4/Rfast/R/frequency.R |only Rfast-1.9.4/Rfast/R/fs.reg.R | 2 Rfast-1.9.4/Rfast/R/ftest.R | 5 Rfast-1.9.4/Rfast/R/ftests.R | 1 Rfast-1.9.4/Rfast/R/g2.R |only Rfast-1.9.4/Rfast/R/gamma.R |only Rfast-1.9.4/Rfast/R/gammacon.R | 1 Rfast-1.9.4/Rfast/R/gammamle.R | 1 Rfast-1.9.4/Rfast/R/gammanb.R | 1 Rfast-1.9.4/Rfast/R/gammanb.pred.R | 1 Rfast-1.9.4/Rfast/R/gammareg.R | 1 Rfast-1.9.4/Rfast/R/gammaregs.R | 1 Rfast-1.9.4/Rfast/R/gaussian.nb.R | 1 Rfast-1.9.4/Rfast/R/gaussiannb.pred.R | 1 Rfast-1.9.4/Rfast/R/gchi2Test.R | 1 Rfast-1.9.4/Rfast/R/geom.anova.R | 5 Rfast-1.9.4/Rfast/R/geom.anovas.R | 1 Rfast-1.9.4/Rfast/R/geom.mle.R | 1 Rfast-1.9.4/Rfast/R/geom.nb.R | 1 Rfast-1.9.4/Rfast/R/geom.regs.R | 1 Rfast-1.9.4/Rfast/R/geomnb.pred.R | 1 Rfast-1.9.4/Rfast/R/ginis.R | 5 Rfast-1.9.4/Rfast/R/glm_logistic.R | 1 Rfast-1.9.4/Rfast/R/glm_poisson.R | 1 Rfast-1.9.4/Rfast/R/group.R | 54 + Rfast-1.9.4/Rfast/R/group.med.R | 2 Rfast-1.9.4/Rfast/R/groupcorrels.R | 1 Rfast-1.9.4/Rfast/R/gumbel.mle.R | 1 Rfast-1.9.4/Rfast/R/halfnorm.mle.R | 1 Rfast-1.9.4/Rfast/R/hd.eigen.R | 1 Rfast-1.9.4/Rfast/R/hsecant01.mle.R | 1 Rfast-1.9.4/Rfast/R/iag.mle.R | 1 Rfast-1.9.4/Rfast/R/ibeta.mle.R | 1 Rfast-1.9.4/Rfast/R/invdir.mle.R | 1 Rfast-1.9.4/Rfast/R/invgauss.mle.R | 1 Rfast-1.9.4/Rfast/R/invgauss.reg.R | 1 Rfast-1.9.4/Rfast/R/invgauss.regs.R | 1 Rfast-1.9.4/Rfast/R/is.R |only Rfast-1.9.4/Rfast/R/iterator.R | 1 Rfast-1.9.4/Rfast/R/james.R | 1 Rfast-1.9.4/Rfast/R/knn.R | 2 Rfast-1.9.4/Rfast/R/knn.cv.R | 2 Rfast-1.9.4/Rfast/R/kruskaltest.R | 3 Rfast-1.9.4/Rfast/R/kruskaltests.R | 1 Rfast-1.9.4/Rfast/R/kuiper.R | 1 Rfast-1.9.4/Rfast/R/kurt.R | 1 Rfast-1.9.4/Rfast/R/kurt.test2.R | 1 Rfast-1.9.4/Rfast/R/laplace.mle.R | 1 Rfast-1.9.4/Rfast/R/lindley.mle.R | 1 Rfast-1.9.4/Rfast/R/list.ftests.R | 1 Rfast-1.9.4/Rfast/R/lmfit.R | 1 Rfast-1.9.4/Rfast/R/logcauchy.mle.R | 1 Rfast-1.9.4/Rfast/R/logical.R |only Rfast-1.9.4/Rfast/R/logistic.cat1.R | 1 Rfast-1.9.4/Rfast/R/logistic.mle.R | 1 Rfast-1.9.4/Rfast/R/logistic_only.R | 2 Rfast-1.9.4/Rfast/R/logitnorm.mle.R | 1 Rfast-1.9.4/Rfast/R/loglogistic.mle.R | 1 Rfast-1.9.4/Rfast/R/lognorm.mle.R | 1 Rfast-1.9.4/Rfast/R/logseries.mle.R | 1 Rfast-1.9.4/Rfast/R/lomax.mle.R | 1 Rfast-1.9.4/Rfast/R/mad2.R | 18 Rfast-1.9.4/Rfast/R/mahala.R | 2 Rfast-1.9.4/Rfast/R/match.coefs.R | 1 Rfast-1.9.4/Rfast/R/matrix.R |only Rfast-1.9.4/Rfast/R/matrnorm.R | 1 Rfast-1.9.4/Rfast/R/maxboltz.mle.R | 1 Rfast-1.9.4/Rfast/R/mcnemar.R | 1 Rfast-1.9.4/Rfast/R/mcnemars.R | 1 Rfast-1.9.4/Rfast/R/median.R |only Rfast-1.9.4/Rfast/R/mediandir.R | 1 Rfast-1.9.4/Rfast/R/min_max.R | 55 + Rfast-1.9.4/Rfast/R/multinom.mle.R | 1 Rfast-1.9.4/Rfast/R/multinom.nb.R | 2 Rfast-1.9.4/Rfast/R/multinom.reg.R | 1 Rfast-1.9.4/Rfast/R/multinom.regs.R | 1 Rfast-1.9.4/Rfast/R/multinomnb.pred.R | 1 Rfast-1.9.4/Rfast/R/multivmf.mle.R | 1 Rfast-1.9.4/Rfast/R/mv.eeltest1.R | 3 Rfast-1.9.4/Rfast/R/mv.eeltest2.R | 1 Rfast-1.9.4/Rfast/R/mvbetas.R | 6 Rfast-1.9.4/Rfast/R/mvkurtosis.R | 1 Rfast-1.9.4/Rfast/R/mvlnorm.mle.R | 1 Rfast-1.9.4/Rfast/R/mvnorm.mle.R | 1 Rfast-1.9.4/Rfast/R/mvt.mle.R | 1 Rfast-1.9.4/Rfast/R/negative.R | 2 Rfast-1.9.4/Rfast/R/negbin.mle.R | 1 Rfast-1.9.4/Rfast/R/normal.mle.R | 1 Rfast-1.9.4/Rfast/R/normlog.mle.R | 1 Rfast-1.9.4/Rfast/R/normlog.reg.R | 1 Rfast-1.9.4/Rfast/R/normlog.regs.R | 2 Rfast-1.9.4/Rfast/R/nth.R | 18 Rfast-1.9.4/Rfast/R/odds.R | 1 Rfast-1.9.4/Rfast/R/odds.ratio.R | 1 Rfast-1.9.4/Rfast/R/omp.R | 16 Rfast-1.9.4/Rfast/R/ompr.R | 8 Rfast-1.9.4/Rfast/R/ordinal.mle.R | 1 Rfast-1.9.4/Rfast/R/pareto.mle.R | 1 Rfast-1.9.4/Rfast/R/pc.skel.R | 1 Rfast-1.9.4/Rfast/R/percent.ttest.R | 1 Rfast-1.9.4/Rfast/R/percent.ttests.R | 1 Rfast-1.9.4/Rfast/R/permcor.R | 1 Rfast-1.9.4/Rfast/R/permutation_combination.R |only Rfast-1.9.4/Rfast/R/pois.test.R | 1 Rfast-1.9.4/Rfast/R/poisdisp.test.R | 1 Rfast-1.9.4/Rfast/R/poisson.anova.R | 3 Rfast-1.9.4/Rfast/R/poisson.anovas.R | 1 Rfast-1.9.4/Rfast/R/poisson.cat1.R | 1 Rfast-1.9.4/Rfast/R/poisson.mle.R | 1 Rfast-1.9.4/Rfast/R/poisson.nb.R | 1 Rfast-1.9.4/Rfast/R/poisson_only.R | 2 Rfast-1.9.4/Rfast/R/poissonnb.pred.R | 1 Rfast-1.9.4/Rfast/R/poly.cor.R | 1 Rfast-1.9.4/Rfast/R/pooled.cov.R | 2 Rfast-1.9.4/Rfast/R/positive.R | 2 Rfast-1.9.4/Rfast/R/positive.negative.R | 2 Rfast-1.9.4/Rfast/R/prods.R |only Rfast-1.9.4/Rfast/R/prop.reg.R | 1 Rfast-1.9.4/Rfast/R/prop.regs.R | 1 Rfast-1.9.4/Rfast/R/proptest.R | 1 Rfast-1.9.4/Rfast/R/proptests.R | 1 Rfast-1.9.4/Rfast/R/qpois.reg.R | 1 Rfast-1.9.4/Rfast/R/qpois.regs.R | 1 Rfast-1.9.4/Rfast/R/quasi.poisson_only.R | 1 Rfast-1.9.4/Rfast/R/quasipoisson.anova.R | 5 Rfast-1.9.4/Rfast/R/quasipoisson.anovas.R | 1 Rfast-1.9.4/Rfast/R/racg.R | 1 Rfast-1.9.4/Rfast/R/rayleigh.mle.R | 1 Rfast-1.9.4/Rfast/R/rbing.R | 2 Rfast-1.9.4/Rfast/R/rbingham.R | 1 Rfast-1.9.4/Rfast/R/regression.R | 1 Rfast-1.9.4/Rfast/R/rel.risk.R | 1 Rfast-1.9.4/Rfast/R/replicate.R |only Rfast-1.9.4/Rfast/R/rint.mle.R | 1 Rfast-1.9.4/Rfast/R/rint.reg.R | 1 Rfast-1.9.4/Rfast/R/rint.regbx.R | 1 Rfast-1.9.4/Rfast/R/rint.regs.R | 1 Rfast-1.9.4/Rfast/R/rm.anova.R | 1 Rfast-1.9.4/Rfast/R/rm.anovas.R | 1 Rfast-1.9.4/Rfast/R/rm.lines.R | 1 Rfast-1.9.4/Rfast/R/rmdp.R | 1 Rfast-1.9.4/Rfast/R/rmvlaplace.R | 1 Rfast-1.9.4/Rfast/R/rmvnorm.R | 1 Rfast-1.9.4/Rfast/R/rmvt.R | 1 Rfast-1.9.4/Rfast/R/rowcvs.R | 1 Rfast-1.9.4/Rfast/R/rowhameans.R | 1 Rfast-1.9.4/Rfast/R/rowmeans.R | 2 Rfast-1.9.4/Rfast/R/rowrange.R | 2 Rfast-1.9.4/Rfast/R/rowsums.R | 2 Rfast-1.9.4/Rfast/R/rvmf.R | 1 Rfast-1.9.4/Rfast/R/rvonmises.R | 1 Rfast-1.9.4/Rfast/R/score.betaregs.R | 23 Rfast-1.9.4/Rfast/R/score.expregs.R | 1 Rfast-1.9.4/Rfast/R/score.gammaregs.R | 19 Rfast-1.9.4/Rfast/R/score.geomregs.R | 2 Rfast-1.9.4/Rfast/R/score.glms.R | 14 Rfast-1.9.4/Rfast/R/score.invgaussregs.R | 19 Rfast-1.9.4/Rfast/R/score.multinomregs.R | 1 Rfast-1.9.4/Rfast/R/score.negbinregs.R | 25 Rfast-1.9.4/Rfast/R/score.weibregs.R | 23 Rfast-1.9.4/Rfast/R/score.ztpregs.R | 21 Rfast-1.9.4/Rfast/R/sftest.R | 1 Rfast-1.9.4/Rfast/R/sftests.R | 3 Rfast-1.9.4/Rfast/R/skew.R | 1 Rfast-1.9.4/Rfast/R/skew.test2.R | 1 Rfast-1.9.4/Rfast/R/sort_unique.R | 5 Rfast-1.9.4/Rfast/R/sourceR.R | 2 Rfast-1.9.4/Rfast/R/sourceRd.R | 2 Rfast-1.9.4/Rfast/R/spat.med.R | 2 Rfast-1.9.4/Rfast/R/spatmed.reg.R | 1 Rfast-1.9.4/Rfast/R/spdinv.R | 1 Rfast-1.9.4/Rfast/R/spml.mle.R | 1 Rfast-1.9.4/Rfast/R/spml.reg.R | 1 Rfast-1.9.4/Rfast/R/spml.regs.R | 1 Rfast-1.9.4/Rfast/R/squareform.R | 2 Rfast-1.9.4/Rfast/R/sscov.R | 1 Rfast-1.9.4/Rfast/R/standardise.R | 1 Rfast-1.9.4/Rfast/R/system_and_package.R |only Rfast-1.9.4/Rfast/R/tmle.R | 1 Rfast-1.9.4/Rfast/R/tobit.mle.R | 1 Rfast-1.9.4/Rfast/R/topological_sort.R | 1 Rfast-1.9.4/Rfast/R/total.dist.R | 2 Rfast-1.9.4/Rfast/R/total.dista.R | 2 Rfast-1.9.4/Rfast/R/triangular.R |only Rfast-1.9.4/Rfast/R/ttest.R | 1 Rfast-1.9.4/Rfast/R/ttest1.R | 1 Rfast-1.9.4/Rfast/R/ttest2.R | 2 Rfast-1.9.4/Rfast/R/ttests.R | 1 Rfast-1.9.4/Rfast/R/ttests.pairs.R | 1 Rfast-1.9.4/Rfast/R/twoway.anova.R | 5 Rfast-1.9.4/Rfast/R/twoway.anovas.R | 1 Rfast-1.9.4/Rfast/R/ufactor.R | 2 Rfast-1.9.4/Rfast/R/univglms.R | 1 Rfast-1.9.4/Rfast/R/univglms2.R | 1 Rfast-1.9.4/Rfast/R/var2test.R | 1 Rfast-1.9.4/Rfast/R/var2tests.R | 1 Rfast-1.9.4/Rfast/R/varcomps.mle.R | 3 Rfast-1.9.4/Rfast/R/varcomps.mom.R | 3 Rfast-1.9.4/Rfast/R/vartest.R | 1 Rfast-1.9.4/Rfast/R/vartests.R | 1 Rfast-1.9.4/Rfast/R/vecdist.R | 2 Rfast-1.9.4/Rfast/R/vm.mle.R | 2 Rfast-1.9.4/Rfast/R/vmf.mle.R | 1 Rfast-1.9.4/Rfast/R/watson.R | 1 Rfast-1.9.4/Rfast/R/weib.reg.R | 2 Rfast-1.9.4/Rfast/R/weibull.mle.R | 1 Rfast-1.9.4/Rfast/R/which.is.R | 2 Rfast-1.9.4/Rfast/R/wigner.mle.R | 1 Rfast-1.9.4/Rfast/R/wrapcauchy.mle.R | 1 Rfast-1.9.4/Rfast/R/yule.R | 1 Rfast-1.9.4/Rfast/R/zip.mle.R | 1 Rfast-1.9.4/Rfast/R/ztp.mle.R | 1 Rfast-1.9.4/Rfast/man/AddToNamespace.Rd | 7 Rfast-1.9.4/Rfast/man/Rfast-package.Rd | 25 Rfast-1.9.4/Rfast/man/as.Rfast.function.Rd | 2 Rfast-1.9.4/Rfast/man/boot.ttest2.Rd | 6 Rfast-1.9.4/Rfast/man/checkNamespace.Rd | 10 Rfast-1.9.4/Rfast/man/colVars.Rd | 3 Rfast-1.9.4/Rfast/man/data.frame.to_matrix.Rd | 2 Rfast-1.9.4/Rfast/man/eel.test1.Rd | 6 Rfast-1.9.4/Rfast/man/eel.test2.Rd | 6 Rfast-1.9.4/Rfast/man/group.sum.Rd | 7 Rfast-1.9.4/Rfast/man/group.var.Rd | 2 Rfast-1.9.4/Rfast/man/logistic_only.Rd | 24 Rfast-1.9.4/Rfast/man/mv.eeltest1.Rd | 5 Rfast-1.9.4/Rfast/man/mv.eeltest2.Rd | 2 Rfast-1.9.4/Rfast/man/normlog.regs.Rd | 28 Rfast-1.9.4/Rfast/man/ordinal.mle.Rd | 2 Rfast-1.9.4/Rfast/man/permcor.Rd | 2 Rfast-1.9.4/Rfast/man/read.directory.Rd | 2 Rfast-1.9.4/Rfast/man/score.glms.Rd | 44 + Rfast-1.9.4/Rfast/man/sort_mat.Rd | 2 Rfast-1.9.4/Rfast/src/add_to_namespace.cpp | 9 Rfast-1.9.4/Rfast/src/check.cpp | 111 +-- Rfast-1.9.4/Rfast/src/init.c | 8 Rfast-1.9.4/Rfast/src/logistic_only.cpp | 12 Rfast-1.9.4/Rfast/src/read.cpp | 2 Rfast-1.9.4/Rfast/src/system_files.cpp | 144 ++++ Rfast-1.9.4/Rfast/src/system_files.h | 6 Rfast-1.9.4/Rfast/src/templates.h | 11 490 files changed, 1586 insertions(+), 837 deletions(-)
Title: Tools for Epidemiologists
Description: Provides set of functions aimed at epidemiologists.
They include commands for measures of association and impact for case control studies and cohort studies.
They may be particularly useful for outbreak investigations and include univariate and stratified analyses.
The functions for cohort studies include the CS(), CSTable() and CSInter() commands.
The functions for case control studies include the CC(), CCTable() and CCInter() commands.
Author: Jean Pierre Decorps [aut, cre],
Esther Kissling [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Diff between EpiStats versions 1.2-2 dated 2019-05-24 and 1.3-1 dated 2019-05-24
DESCRIPTION | 6 +++--- MD5 | 4 ++-- inst/doc/EpiStats.pdf |binary 3 files changed, 5 insertions(+), 5 deletions(-)
Title: Discrete Bayesian Additive Regression Trees Sampler
Description: Fits Bayesian additive regression trees (BART; Chipman, George, and McCulloch (2010) <doi:10.1214/09-AOAS285>) while allowing the updating of predictors or response so that BART can be incorporated as a conditional model in a Gibbs/MH sampler. Also serves as a drop-in replacement for package 'BayesTree'.
Author: Vincent Dorie [aut, cre],
Hugh Chipman [aut],
Robert McCulloch [aut]
Maintainer: Vincent Dorie <vdorie@gmail.com>
Diff between dbarts versions 0.9-11 dated 2019-04-20 and 0.9-12 dated 2019-05-24
dbarts-0.9-11/dbarts/src/include/misc/types.h |only dbarts-0.9-12/dbarts/DESCRIPTION | 8 - dbarts-0.9-12/dbarts/MD5 | 79 ++++------ dbarts-0.9-12/dbarts/R/dbarts.R | 8 + dbarts-0.9-12/dbarts/R/rbart.R | 68 +++++--- dbarts-0.9-12/dbarts/configure | 18 +- dbarts-0.9-12/dbarts/configure.ac | 2 dbarts-0.9-12/dbarts/inst/NEWS.Rd | 7 dbarts-0.9-12/dbarts/inst/include/dbarts/R_C_interface.hpp | 2 dbarts-0.9-12/dbarts/inst/include/dbarts/bartFit.hpp | 1 dbarts-0.9-12/dbarts/src/Makevars.in | 2 dbarts-0.9-12/dbarts/src/Makevars.win | 2 dbarts-0.9-12/dbarts/src/R_C_interface.cpp | 5 dbarts-0.9-12/dbarts/src/R_interface.cpp | 2 dbarts-0.9-12/dbarts/src/R_interface_sampler.cpp | 28 ++- dbarts-0.9-12/dbarts/src/R_interface_sampler.hpp | 1 dbarts-0.9-12/dbarts/src/config.hpp.win | 4 dbarts-0.9-12/dbarts/src/dbarts/bartFit.cpp | 13 + dbarts-0.9-12/dbarts/src/dbarts/birthDeathRule.cpp | 71 ++++---- dbarts-0.9-12/dbarts/src/dbarts/config.hpp.win | 4 dbarts-0.9-12/dbarts/src/dbarts/node.cpp | 14 - dbarts-0.9-12/dbarts/src/external/config.h.win | 4 dbarts-0.9-12/dbarts/src/include/misc/alloca.h | 32 +--- dbarts-0.9-12/dbarts/src/makeModelMatrixFromDataFrame.c | 8 - dbarts-0.9-12/dbarts/src/misc/Makefile | 12 - dbarts-0.9-12/dbarts/src/misc/config.h.win | 4 dbarts-0.9-12/dbarts/src/misc/moments.c | 4 dbarts-0.9-12/dbarts/tests/testthat/test-01-dbartsDataArgs.R | 18 +- dbarts-0.9-12/dbarts/tests/testthat/test-02-dbartsModelArgs.R | 2 dbarts-0.9-12/dbarts/tests/testthat/test-03-dbartsControl.R | 2 dbarts-0.9-12/dbarts/tests/testthat/test-04-continuousResponse.R | 4 dbarts-0.9-12/dbarts/tests/testthat/test-05-binaryResponse.R | 6 dbarts-0.9-12/dbarts/tests/testthat/test-06-dbartsSampler.R | 8 - dbarts-0.9-12/dbarts/tests/testthat/test-07-multithreaded.R | 2 dbarts-0.9-12/dbarts/tests/testthat/test-08-xbart.R | 2 dbarts-0.9-12/dbarts/tests/testthat/test-09-predict.R | 4 dbarts-0.9-12/dbarts/tests/testthat/test-12-multipleChains.R | 2 dbarts-0.9-12/dbarts/tests/testthat/test-13-bart2.R | 2 dbarts-0.9-12/dbarts/tests/testthat/test-14-rbart.R | 53 ++++++ dbarts-0.9-12/dbarts/tests/testthat/test-15-simd.R | 4 dbarts-0.9-12/dbarts/tests/testthat/test-16-pdbart.R | 7 41 files changed, 315 insertions(+), 204 deletions(-)
Title: Binary Choice Models with Fixed Effects
Description: Estimates fixed effects binary choice models (logit and probit) with potentially many
individual fixed effects and computes average partial effects. Incidental parameter bias can be
reduced with an asymptotic bias-correction proposed by Fernandez-Val (2009)
<doi:10.1016/j.jeconom.2009.02.007>.
Author: Amrei Stammann [aut, cre],
Daniel Czarnowske [aut] (<https://orcid.org/0000-0002-0030-929X>),
Florian Heiss [aut],
Daniel McFadden [ctb]
Maintainer: Amrei Stammann <amrei.stammann@hhu.de>
Diff between bife versions 0.5 dated 2018-03-07 and 0.6 dated 2019-05-24
bife-0.5/bife/R/acs.R |only bife-0.5/bife/R/apeff_bife.R |only bife-0.5/bife/R/coef_bife.R |only bife-0.5/bife/R/predict_bife.R |only bife-0.5/bife/R/print_bife.R |only bife-0.5/bife/R/print_summary_bife.R |only bife-0.5/bife/R/results_acs.R |only bife-0.5/bife/R/results_psid.R |only bife-0.5/bife/R/summary_bife.R |only bife-0.5/bife/R/time_n.R |only bife-0.5/bife/R/time_t.R |only bife-0.5/bife/R/unload.R |only bife-0.5/bife/R/vcov_bife.R |only bife-0.5/bife/build/partial.rdb |only bife-0.5/bife/data/acs.rda |only bife-0.5/bife/data/datalist |only bife-0.5/bife/data/results_acs.rda |only bife-0.5/bife/data/results_psid.rda |only bife-0.5/bife/data/time_n.rda |only bife-0.5/bife/data/time_t.rda |only bife-0.5/bife/inst/doc/bife_introduction.R |only bife-0.5/bife/inst/doc/bife_introduction.Rmd |only bife-0.5/bife/inst/doc/bife_introduction.html |only bife-0.5/bife/man/acs.Rd |only bife-0.5/bife/man/apeff_bife.Rd |only bife-0.5/bife/man/bife-package.Rd |only bife-0.5/bife/man/results_acs.Rd |only bife-0.5/bife/man/results_psid.Rd |only bife-0.5/bife/man/time_n.Rd |only bife-0.5/bife/man/time_t.Rd |only bife-0.5/bife/vignettes/bife_introduction.Rmd |only bife-0.6/bife/DESCRIPTION | 25 bife-0.6/bife/MD5 | 89 +- bife-0.6/bife/NAMESPACE | 24 bife-0.6/bife/NEWS | 13 bife-0.6/bife/R/RcppExports.R | 32 bife-0.6/bife/R/bias_corr.R |only bife-0.6/bife/R/bife.R | 616 ++++++++++-------- bife-0.6/bife/R/generics.R |only bife-0.6/bife/R/get_APEs.R |only bife-0.6/bife/R/helpers.R |only bife-0.6/bife/R/psid.R | 18 bife-0.6/bife/build/vignette.rds |binary bife-0.6/bife/inst/doc/howto.R |only bife-0.6/bife/inst/doc/howto.Rmd |only bife-0.6/bife/inst/doc/howto.html |only bife-0.6/bife/man/bias_corr.Rd |only bife-0.6/bife/man/bife.Rd | 177 +---- bife-0.6/bife/man/bife_control.Rd |only bife-0.6/bife/man/coef.bife.Rd | 28 bife-0.6/bife/man/coef.bifeAPEs.Rd |only bife-0.6/bife/man/fitted.bife.Rd |only bife-0.6/bife/man/get_APEs.Rd |only bife-0.6/bife/man/predict.bife.Rd | 66 - bife-0.6/bife/man/print.bife.Rd | 19 bife-0.6/bife/man/print.bifeAPEs.Rd |only bife-0.6/bife/man/print.summary.bife.Rd | 20 bife-0.6/bife/man/print.summary.bifeAPEs.Rd |only bife-0.6/bife/man/psid.Rd | 14 bife-0.6/bife/man/summary.bife.Rd | 30 bife-0.6/bife/man/summary.bifeAPEs.Rd |only bife-0.6/bife/man/vcov.bife.Rd | 25 bife-0.6/bife/man/vcov.bifeAPEs.Rd |only bife-0.6/bife/src/Makevars | 13 bife-0.6/bife/src/Makevars.win | 13 bife-0.6/bife/src/RcppExports.cpp | 144 ++-- bife-0.6/bife/src/bias_corr.cpp |only bife-0.6/bife/src/bife.cpp | 885 ++------------------------ bife-0.6/bife/vignettes/howto.Rmd |only bife-0.6/bife/vignettes/refs.bib | 116 ++- 70 files changed, 871 insertions(+), 1496 deletions(-)
Title: Reproducible Data Retrieval from the ICPSR Archive
Description: Reproducible, programmatic retrieval of datasets from the
Inter-university Consortium for Political and Social Research archive.
Author: Frederick Solt [aut, cre],
Kellen Gracey [aut],
Eric Persson [ctb],
Joanna Pepin [ctb],
J. Hathaway [ctb]
Maintainer: Frederick Solt <frederick-solt@uiowa.edu>
Diff between icpsrdata versions 0.3.0 dated 2016-12-08 and 0.4.0 dated 2019-05-24
DESCRIPTION | 20 +- MD5 | 20 +- NAMESPACE | 1 NEWS.md | 4 R/icpsrdownload.R | 64 +++++-- README.md | 4 build/vignette.rds |binary inst/doc/icpsrdata-vignette.Rmd | 4 inst/doc/icpsrdata-vignette.html | 333 +++++++++++++++++++++++++++++++++------ man/icpsr_download.Rd | 12 + vignettes/icpsrdata-vignette.Rmd | 4 11 files changed, 375 insertions(+), 91 deletions(-)
Title: Storage Management in 'Azure'
Description: Manage storage in Microsoft's 'Azure' cloud: <https://azure.microsoft.com/services/storage>. On the admin side, 'AzureStor' includes features to create, modify and delete storage accounts. On the client side, it includes an interface to blob storage, file storage, and 'Azure Data Lake Storage Gen2': upload and download files and blobs; list containers and files/blobs; create containers; and so on. Authenticated access to storage is supported, via either a shared access key or a shared access signature (SAS).
Author: Hong Ooi [aut, cre],
Microsoft [cph]
Maintainer: Hong Ooi <hongooi@microsoft.com>
Diff between AzureStor versions 2.0.1 dated 2019-03-21 and 2.0.2 dated 2019-05-24
DESCRIPTION | 10 MD5 | 64 +-- NEWS.md | 8 R/AzureStor.R | 3 R/add_methods.R | 2 R/adls_client_funcs.R | 14 R/adls_transfer_internal.R | 95 ++-- R/azcopy.R | 2 R/blob_client_funcs.R | 15 R/blob_transfer_internal.R | 85 ++-- R/client_endpoint.R | 13 R/file_client_funcs.R | 12 R/file_transfer_internal.R | 114 ++--- R/normalize_src.R |only R/progress_bar.R |only R/storage_utils.R | 31 + R/transfer_generics.R | 2 README.md | 6 inst/doc/generics.html | 608 +++++++++++++++++----------- inst/doc/intro.html | 885 ++++++++++++++++++++++-------------------- inst/doc/intro.rmd | 3 man/adls.Rd | 13 man/adls_filesystem.Rd | 2 man/azcopy.Rd | 2 man/blob.Rd | 13 man/blob_container.Rd | 2 man/create_storage_account.Rd | 2 man/file.Rd | 13 man/file_transfer.Rd | 2 man/storage_endpoint.Rd | 13 tests/testthat/test02_blob.R | 99 ++++ tests/testthat/test03_file.R | 99 ++++ tests/testthat/test04_adls.R | 99 ++++ vignettes/intro.rmd | 3 34 files changed, 1453 insertions(+), 881 deletions(-)
Title: R Interface to the Species+ Database
Description: A programmatic interface to the Species+ <https://speciesplus.net/> database via the Species+/CITES Checklist API <https://api.speciesplus.net/>.
Author: Jonas Geschke [aut] (<https://orcid.org/0000-0002-5654-9313>),
Kevin Cazelles [aut, cre] (<https://orcid.org/0000-0001-6619-9874>),
Ignasi Bartomeus [aut] (<https://orcid.org/0000-0001-7893-4389>),
Jonathan Goldenberg [ctb],
Marie-Bé Leduc [ctb],
Yasmine Verzelen [ctb],
Noam Ross [rev],
Margaret Siple [rev]
Maintainer: Kevin Cazelles <kevin.cazelles@gmail.com>
Diff between rcites versions 1.0.0 dated 2018-11-17 and 1.0.1 dated 2019-05-24
rcites-1.0.0/rcites/inst/doc/bulk_analysis.R |only rcites-1.0.0/rcites/inst/doc/bulk_analysis.Rmd |only rcites-1.0.0/rcites/inst/doc/bulk_analysis.html |only rcites-1.0.0/rcites/inst/doc/elephant.R |only rcites-1.0.0/rcites/inst/doc/elephant.Rmd |only rcites-1.0.0/rcites/inst/doc/elephant.html |only rcites-1.0.0/rcites/inst/doc/get_started.R |only rcites-1.0.0/rcites/inst/doc/get_started.Rmd |only rcites-1.0.0/rcites/inst/doc/get_started.html |only rcites-1.0.0/rcites/vignettes/bulk_analysis.Rmd |only rcites-1.0.0/rcites/vignettes/elephant.Rmd |only rcites-1.0.0/rcites/vignettes/get_started.Rmd |only rcites-1.0.1/rcites/DESCRIPTION | 10 - rcites-1.0.1/rcites/MD5 | 58 +++++----- rcites-1.0.1/rcites/NAMESPACE | 2 rcites-1.0.1/rcites/R/print.spp.R | 29 ++--- rcites-1.0.1/rcites/R/set_token.R | 4 rcites-1.0.1/rcites/R/spp_cites_legislation.R | 2 rcites-1.0.1/rcites/R/spp_distributions.R | 2 rcites-1.0.1/rcites/R/spp_eu_legislation.R | 2 rcites-1.0.1/rcites/R/spp_references.R | 2 rcites-1.0.1/rcites/R/spp_taxonconcept.R | 9 + rcites-1.0.1/rcites/R/zzz.R | 87 ++++++++++------ rcites-1.0.1/rcites/README.md | 17 +-- rcites-1.0.1/rcites/build/vignette.rds |binary rcites-1.0.1/rcites/inst/doc/a_get_started.R |only rcites-1.0.1/rcites/inst/doc/a_get_started.Rmd |only rcites-1.0.1/rcites/inst/doc/a_get_started.html |only rcites-1.0.1/rcites/inst/doc/b_elephant.R |only rcites-1.0.1/rcites/inst/doc/b_elephant.Rmd |only rcites-1.0.1/rcites/inst/doc/b_elephant.html |only rcites-1.0.1/rcites/inst/doc/c_bulk_analysis.R |only rcites-1.0.1/rcites/inst/doc/c_bulk_analysis.Rmd |only rcites-1.0.1/rcites/inst/doc/c_bulk_analysis.html |only rcites-1.0.1/rcites/tests/testthat/test-distributions.R | 4 rcites-1.0.1/rcites/tests/testthat/test-legislations.R | 10 - rcites-1.0.1/rcites/tests/testthat/test-pkghelpers.R | 7 - rcites-1.0.1/rcites/tests/testthat/test-references.R | 8 - rcites-1.0.1/rcites/tests/testthat/test-taxonconcept.R | 10 + rcites-1.0.1/rcites/vignettes/a_get_started.Rmd |only rcites-1.0.1/rcites/vignettes/b_elephant.Rmd |only rcites-1.0.1/rcites/vignettes/c_bulk_analysis.Rmd |only 42 files changed, 149 insertions(+), 114 deletions(-)
Title: Functions to Support the ICES Transparent Assessment Framework
Description: Functions to support the ICES Transparent Assessment Framework
<http://taf.ices.dk> to organize data, methods, and results used in ICES
assessments. ICES is an organization facilitating international collaboration
in marine science.
Author: Arni Magnusson [aut, cre],
Colin Millar [aut],
Alexandros Kokkalis [ctb]
Maintainer: Arni Magnusson <arni.magnusson@ices.dk>
Diff between icesTAF versions 3.0-0 dated 2019-04-25 and 3.1-1 dated 2019-05-24
DESCRIPTION | 8 +- MD5 | 43 +++++++------ NAMESPACE | 3 NEWS | 29 ++++++++ R/convert.spaces.R |only R/draft.data.R | 2 R/flr2taf.R | 1 R/icesTAF-package.R | 22 +++--- R/process.bib.R | 162 ++++++++++++++++++++++--------------------------- R/process.inner.R |only R/sam2taf.R |only R/sourceTAF.R | 11 +-- R/taf.bootstrap.R | 80 +++++++++++++----------- data/catage.long.rda |binary data/catage.taf.rda |binary data/catage.xtab.rda |binary data/summary.taf.rda |binary data/taf.colors.rda |binary man/convert.spaces.Rd |only man/flr2taf.Rd | 1 man/icesTAF-package.Rd | 22 +++--- man/process.bib.Rd | 88 +++++++++++++++++--------- man/sam2taf.Rd |only man/sourceTAF.Rd | 5 - man/taf.bootstrap.Rd | 13 +-- 25 files changed, 279 insertions(+), 211 deletions(-)
Title: Robust Geostatistical Analysis of Spatial Data
Description: Provides functions for efficiently fitting linear models with
spatially correlated errors by robust and Gaussian (Restricted)
Maximum Likelihood and for computing robust and customary point
and block external-drift Kriging predictions, along with utility
functions for variogram modelling in ad hoc geostatistical analyses,
model building, model evaluation by cross-validation, (conditional)
simulation of Gaussian processes, unbiased back-transformation of
Kriging predictions of log-transformed data.
Author: Andreas Papritz [cre, aut],
Cornelia Schwierz [ctb]
Maintainer: Andreas Papritz <andreas.papritz@env.ethz.ch>
Diff between georob versions 0.3-9 dated 2019-04-08 and 0.3-10 dated 2019-05-24
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- NEWS | 1 + R/georob.S3methods.R | 7 +++++-- R/georob.simulation.R | 8 ++++++-- inst/doc/georob_vignette.pdf |binary 6 files changed, 21 insertions(+), 13 deletions(-)
Title: Tools for Epidemiologists
Description: Provides set of functions aimed at epidemiologists.
They include commands for measures of association and impact for case control studies and cohort studies.
They may be particularly useful for outbreak investigations and include univariate and stratified analyses.
The functions for cohort studies include the CS(), CSTable() and CSInter() commands.
The functions for case control studies include the CC(), CCTable() and CCInter() commands.
Author: Jean Pierre Decorps [aut, cre],
Esther Kissling [ctb]
Maintainer: Jean Pierre Decorps <jp.decorps@epiconcept.fr>
Diff between EpiStats versions 1.2 dated 2018-10-08 and 1.2-2 dated 2019-05-24
DESCRIPTION | 8 +- MD5 | 40 ++++++------- R/01_EpiFuns.R | 40 ++++++------- R/CCInter_.R | 143 ++++++++++++++++++++++++------------------------- R/CC_.R | 78 +++++++++++++------------- R/CSInter_.R | 71 +++++++++++------------- R/crosstable.R | 12 ++-- README.md | 2 build/vignette.rds |binary inst/doc/EpiStats.R | 84 +++++++++++++++------------- inst/doc/EpiStats.Rmd | 28 +++++---- inst/doc/EpiStats.pdf |binary man/CC.Rd | 11 +-- man/CCInter.Rd | 10 +-- man/CCTable.Rd | 11 +-- man/CS.Rd | 3 - man/CSInter.Rd | 7 +- man/CSTable.Rd | 13 ++-- man/crossTable.Rd | 3 - man/orderFactors.Rd | 3 - vignettes/EpiStats.Rmd | 28 +++++---- 21 files changed, 300 insertions(+), 295 deletions(-)
Title: Fit GLM's with High-Dimensional k-Way Fixed Effects
Description: Provides a routine to concentrate out factors with many levels during the
optimization of the log-likelihood function of the corresponding generalized linear model (glm).
The package is based on the algorithm proposed by Stammann (2018) <arXiv:1707.01815> and is
restricted to glm's that are based on maximum likelihood estimation and non-linear. It also offers
an efficient algorithm to recover estimates of the fixed effects in a post-estimation routine and
includes robust and multi-way clustered standard errors. Further the package provides an
analytical bias-correction for binary choice models (logit and probit) derived by Fernandez-Val
and Weidner (2016) <doi:10.1016/j.jeconom.2015.12.014>.
Author: Amrei Stammann [aut, cre],
Daniel Czarnowske [aut] (<https://orcid.org/0000-0002-0030-929X>)
Maintainer: Amrei Stammann <amrei.stammann@hhu.de>
Diff between alpaca versions 0.3 dated 2019-05-14 and 0.3.1 dated 2019-05-24
alpaca-0.3.1/alpaca/DESCRIPTION | 6 +- alpaca-0.3.1/alpaca/MD5 | 53 ++++++++++++------------- alpaca-0.3.1/alpaca/NAMESPACE | 2 alpaca-0.3.1/alpaca/R/alpaca.R | 4 - alpaca-0.3.1/alpaca/R/biasCorr.R | 30 +------------- alpaca-0.3.1/alpaca/R/feglm.R | 45 +++++++++------------ alpaca-0.3.1/alpaca/R/feglm.nb.R | 28 ++++++------- alpaca-0.3.1/alpaca/R/generics.R | 8 +-- alpaca-0.3.1/alpaca/R/getAPEs.R | 39 +++++++++--------- alpaca-0.3.1/alpaca/R/helpers.R | 28 +++++++++---- alpaca-0.3.1/alpaca/inst/CITATION | 4 - alpaca-0.3.1/alpaca/inst/NEWS.Rd |only alpaca-0.3.1/alpaca/inst/doc/howto.R | 28 ++++++------- alpaca-0.3.1/alpaca/inst/doc/howto.Rmd | 49 ++++++++++------------- alpaca-0.3.1/alpaca/inst/doc/howto.html | 55 ++++++++++---------------- alpaca-0.3.1/alpaca/inst/doc/replication.R | 2 alpaca-0.3.1/alpaca/inst/doc/replication.Rmd | 2 alpaca-0.3.1/alpaca/inst/doc/replication.html | 2 alpaca-0.3.1/alpaca/man/alpaca-package.Rd |only alpaca-0.3.1/alpaca/man/biasCorr.Rd | 8 --- alpaca-0.3.1/alpaca/man/feglm.Rd | 4 - alpaca-0.3.1/alpaca/man/feglm.nb.Rd | 10 ---- alpaca-0.3.1/alpaca/man/feglmControl.Rd | 2 alpaca-0.3.1/alpaca/man/getAPEs.Rd | 12 ++++- alpaca-0.3.1/alpaca/man/predict.feglm.Rd | 2 alpaca-0.3.1/alpaca/vignettes/howto.Rmd | 49 ++++++++++------------- alpaca-0.3.1/alpaca/vignettes/lit.bib | 14 +++--- alpaca-0.3.1/alpaca/vignettes/replication.Rmd | 2 alpaca-0.3/alpaca/man/alpaca.Rd |only 29 files changed, 225 insertions(+), 263 deletions(-)
Title: Utilities for Working with NEON Data
Description: NEON data packages can be accessed through the NEON Data Portal <http://data.neonscience.org>
or through the NEON Data API (see <http://data.neonscience.org/data-api> for documentation). Data delivered from
the Data Portal are provided as monthly zip files packaged within a parent zip file, while individual files
can be accessed from the API. This package provides tools that aid in discovering, downloading, and reformatting
data prior to use in analyses. This includes downloading data via the API, merging data tables by type, and
converting formats. For more information, see the readme file at <https://github.com/NEONScience/NEON-utilities>.
Author: Christine Laney <claney@battelleecology.org>, Claire Lunch <clunch@battelleecology.org>
Maintainer: Claire Lunch <clunch@battelleecology.org>
Diff between neonUtilities versions 1.2.1 dated 2019-03-06 and 1.2.2 dated 2019-05-24
DESCRIPTION | 8 ++++---- MD5 | 26 ++++++++++++++------------ NAMESPACE | 1 + R/byFileAOP.R | 9 ++++++++- R/byTileAOP.R | 9 ++++++++- R/getDatatable.R | 2 +- R/getProductSensors.R | 2 ++ R/getTaxonTable.R | 4 ++-- R/sysdata.rda |binary R/zipsByURI.R |only README.md | 15 +++++++++++++++ man/getDatatable.Rd | 2 +- man/getProductSensors.Rd | 2 ++ man/getTaxonTable.Rd | 4 ++-- man/zipsByURI.Rd |only 15 files changed, 60 insertions(+), 24 deletions(-)
Title: Multivariate Data Analysis for Chemometrics
Description: Package implements projection based methods for preprocessing,
exploring and analysis of multivariate data used in chemometrics.
Author: Sergey Kucheryavskiy
Maintainer: Sergey Kucheryavskiy <svkucheryavski@gmail.com>
Diff between mdatools versions 0.9.1 dated 2018-07-06 and 0.9.4 dated 2019-05-24
DESCRIPTION | 11 +- MD5 | 123 ++++++++++++++++--------------- NAMESPACE | 2 NEWS.md | 17 ++++ R/classres.R | 4 - R/crossval.R | 4 - R/defaults.R | 4 - R/ipls.R | 101 ++++++++------------------ R/mdaplots.R | 4 - R/pca.R | 4 - R/pls.R | 147 +++++++++++++++++++------------------- R/plsda.R | 3 R/prep.R | 22 ++++- README.md | 20 +---- data/pellets.RData |binary data/people.RData |binary data/simdata.RData |binary man/getRegcoeffs.pls.Rd | 7 + man/ipls.Rd | 7 + man/ldecomp.getDistances.Rd | 3 man/mdaplot.Rd | 9 +- man/mdaplot.getAxesLim.Rd | 4 - man/mdaplot.plotAxes.Rd | 6 - man/mdaplot.showLines.Rd | 3 man/mdaplot.showRegressionLine.Rd | 4 - man/mdaplotg.Rd | 15 ++- man/pca.Rd | 7 + man/pca.cal.Rd | 4 - man/pca.mvreplace.Rd | 4 - man/plot.randtest.Rd | 4 - man/plot.regcoeffs.Rd | 6 - man/plotCooman.simcamres.Rd | 4 - man/plotCumVariance.ldecomp.Rd | 4 - man/plotModelDistance.simcam.Rd | 4 - man/plotPerformance.classmodel.Rd | 6 - man/plotPredictions.plsres.Rd | 4 - man/plotPredictions.regres.Rd | 6 - man/plotRMSE.ipls.Rd | 14 +-- man/plotRMSE.regres.Rd | 3 man/plotResiduals.pcares.Rd | 4 - man/plotResiduals.simcares.Rd | 6 - man/plotScores.pca.Rd | 6 - man/plotSelection.ipls.Rd | 5 - man/plotSelectivityRatio.pls.Rd | 4 - man/plotVariance.ldecomp.Rd | 4 - man/plotVariance.pca.Rd | 4 - man/plotVariance.pls.Rd | 7 + man/plotXCumVariance.plsres.Rd | 3 man/plotXResiduals.pls.Rd | 4 - man/plotXScores.plsres.Rd | 3 man/plotYCumVariance.plsres.Rd | 3 man/plotYResiduals.regres.Rd | 4 - man/pls.Rd | 9 +- man/pls.cal.Rd | 5 - man/plsda.Rd | 5 - man/prep.autoscale.Rd | 9 +- man/randtest.Rd | 3 man/selectCompNum.Rd | 4 - man/selectCompNum.pca.Rd | 4 - man/selectCompNum.pls.Rd | 13 ++- man/setResLimits.pca.Rd | 3 man/summary.regcoeffs.Rd | 3 tests/testthat/test_prep.R |only 63 files changed, 376 insertions(+), 333 deletions(-)
More information about climateStability at CRAN
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Title: Bayesian Continual Reassessment Method for Phase I
Dose-Escalation Trials
Description: Implements a wide variety of one- and two-parameter Bayesian CRM
designs. The program can run interactively, allowing the user to enter outcomes
after each cohort has been recruited, or via simulation to assess operating
characteristics.
Author: Michael Sweeting [aut],
Graham Wheeler [aut, cre]
Maintainer: Graham Wheeler <graham.wheeler@ucl.ac.uk>
Diff between bcrm versions 0.5.1 dated 2019-05-22 and 0.5.2 dated 2019-05-24
DESCRIPTION | 11 +++++----- MD5 | 10 ++++----- NEWS | 8 +++++++ R/bcrm-package.R | 2 - R/bcrm.R | 59 ++++++++++++++++++++++++++++++++++++++++--------------- R/posteriors.R | 47 +++++++++++++++++++++++++++++++++++++++++++ 6 files changed, 110 insertions(+), 27 deletions(-)
Title: Bayesian Non- And Semi-Parametric Model Fitting
Description: MCMC algorithms & processing functions for non- and semi-parametric models: 1. Dirichlet process mixtures & 2. spike-slab for multivariate (and univariate) response analysis, with nonparametric models for the means, the variances and the correlation matrix.
Author: Georgios Papageorgiou
Maintainer: Georgios Papageorgiou <gpapageo@gmail.com>
Diff between BNSP versions 2.0.9 dated 2019-05-15 and 2.1.0 dated 2019-05-24
BNSP-2.0.9/BNSP/man/mmvrm.Rd |only BNSP-2.0.9/BNSP/man/mmvrm2mcmc.Rd |only BNSP-2.1.0/BNSP/DESCRIPTION | 10 BNSP-2.1.0/BNSP/MD5 | 42 +- BNSP-2.1.0/BNSP/NAMESPACE | 7 BNSP-2.1.0/BNSP/R/bnpMulti.R | 394 +++++++++++--------- BNSP-2.1.0/BNSP/R/mvrm.R | 699 ------------------------------------ BNSP-2.1.0/BNSP/inst/CITATION | 25 - BNSP-2.1.0/BNSP/man/BNSP-package.Rd | 15 BNSP-2.1.0/BNSP/man/clustering.Rd | 2 BNSP-2.1.0/BNSP/man/continue.Rd | 10 BNSP-2.1.0/BNSP/man/histCorr.Rd | 6 BNSP-2.1.0/BNSP/man/mvrm.Rd | 144 +++++-- BNSP-2.1.0/BNSP/man/mvrm2mcmc.Rd | 4 BNSP-2.1.0/BNSP/man/plot.mvrm.Rd | 8 BNSP-2.1.0/BNSP/man/summary.mvrm.Rd | 3 BNSP-2.1.0/BNSP/src/BNSP_init.c | 4 BNSP-2.1.0/BNSP/src/BayesMult.c | 76 +-- BNSP-2.1.0/BNSP/src/BayesMultG.c | 65 +-- BNSP-2.1.0/BNSP/src/BayesMultGV.c | 70 +-- BNSP-2.1.0/BNSP/src/OneResLtnt.c | 2 BNSP-2.1.0/BNSP/src/mvrmGAM.c | 158 +++++--- BNSP-2.1.0/BNSP/src/pdfs.h | 2 23 files changed, 595 insertions(+), 1151 deletions(-)
Title: Incremental Calculation of Dynamic Time Warping
Description: The Dynamic Time Warping (DTW) distance measure for time series allows non-linear alignments of time series to match similar patterns in time series of different lengths and or different speeds. IncDTW is characterized by (1) the incremental calculation of DTW (reduces runtime complexity to a linear level for updating the DTW distance) - especially for life data streams or subsequence matching, (2) the vector based implementation of DTW which is faster because no matrices are allocated (reduces the space complexity from a quadratic to a linear level in the number of observations) - for all runtime intensive DTW computations, (3) the subsequence matching algorithm runDTW, that efficiently finds the k-NN to a query pattern in a long time series, and (4) C++ in the heart. For details about DTW see the original paper "Dynamic programming algorithm optimization for spoken word recognition" by Sakoe and Chiba (1978) <DOI:10.1109/TASSP.1978.1163055>.
Author: Maximilian Leodolter
Maintainer: Maximilian Leodolter <maximilian.leodolter@gmail.com>
Diff between IncDTW versions 1.1.0 dated 2019-04-08 and 1.1.1 dated 2019-05-24
IncDTW-1.1.0/IncDTW/R/data_preparation.R |only IncDTW-1.1.0/IncDTW/R/notes.R |only IncDTW-1.1.1/IncDTW/DESCRIPTION | 8 IncDTW-1.1.1/IncDTW/MD5 | 26 IncDTW-1.1.1/IncDTW/R/RcppExports.R | 20 IncDTW-1.1.1/IncDTW/R/dtw.R | 172 - IncDTW-1.1.1/IncDTW/inst/doc/Incremental_Dynamic_Time_Warping.html | 287 - IncDTW-1.1.1/IncDTW/man/drink_glass.Rd | 2 IncDTW-1.1.1/IncDTW/man/rundtw.Rd | 69 IncDTW-1.1.1/IncDTW/src/RcppExports.cpp | 74 IncDTW-1.1.1/IncDTW/src/init.c | 14 IncDTW-1.1.1/IncDTW/src/rundtw.cpp | 1578 +++++++++- IncDTW-1.1.1/IncDTW/tests/testthat/test_rundtw_multiv.R | 28 IncDTW-1.1.1/IncDTW/tests/testthat/test_rundtw_multiv_znorm.R |only IncDTW-1.1.1/IncDTW/tests/testthat/test_rundtw_univ.R | 86 IncDTW-1.1.1/IncDTW/tests/testthat/test_rundtw_univ_znorm.R |only 16 files changed, 2034 insertions(+), 330 deletions(-)
Title: Interface to the 'g:Profiler' Toolset
Description: A toolset for functional enrichment analysis and visualization, gene/protein/SNP identifier conversion and mapping orthologous genes across species via 'g:Profiler' (<https://biit.cs.ut.ee/gprofiler>).
The main tools are:
(1) 'g:GOSt' - functional enrichment analysis and visualization of gene lists;
(2) 'g:Convert' - gene/protein/transcript identifier conversion across various namespaces;
(3) 'g:Orth' - orthology search across species;
(4) 'g:SNPense' - mapping SNP rs identifiers to chromosome positions, genes and variant effects
This package is an R interface corresponding to the 2019 update of 'g:Profiler' and provides access to 'g:Profiler' for versions 'e94_eg41_p11' and higher. See the package 'gProfileR' for accessing older versions from the 'g:Profiler' toolset.
Author: Liis Kolberg <liis.kolberg@ut.ee>, Uku Raudvere <uku.raudvere@ut.ee>
Maintainer: Liis Kolberg <liis.kolberg@ut.ee>
Diff between gprofiler2 versions 0.1.3 dated 2019-04-23 and 0.1.4 dated 2019-05-24
DESCRIPTION | 6 - MD5 | 11 +- NAMESPACE | 1 R/gprofiler2.R | 221 ++++++++++++++++++++++++++++++++++++++++++----- man/gost.Rd | 10 +- man/publish_gosttable.Rd |only man/set_base_url.Rd | 4 7 files changed, 218 insertions(+), 35 deletions(-)
Title: Searching for Optimal Clustering Procedure for a Data Set
Description: Distance measures (GDM1, GDM2, Sokal-Michener, Bray-Curtis, for symbolic interval-valued data), cluster quality indices (Calinski-Harabasz, Baker-Hubert, Hubert-Levine, Silhouette, Krzanowski-Lai, Hartigan, Gap, Davies-Bouldin), data normalization formulas (metric data, interval-valued symbolic data), data generation (typical and non-typical data), HINoV method, replication analysis, linear ordering methods, spectral clustering, agreement indices between two partitions, plot functions (for categorical and symbolic interval-valued data).
(MILLIGAN, G.W., COOPER, M.C. (1985) <doi:10.1007/BF02294245>,
HUBERT, L., ARABIE, P. (1985) <doi:10.1007%2FBF01908075>,
RAND, W.M. (1971) <doi:10.1080/01621459.1971.10482356>,
JAJUGA, K., WALESIAK, M. (2000) <doi:10.1007/978-3-642-57280-7_11>,
MILLIGAN, G.W., COOPER, M.C. (1988) <doi:10.1007/BF01897163>,
JAJUGA, K., WALESIAK, M., BAK, A. (2003) <doi:10.1007/978-3-642-55721-7_12>,
DAVIES, D.L., BOULDIN, D.W. (1979) <doi:10.1109/TPAMI.1979.4766909>,
CALINSKI, T., HARABASZ, J. (1974) <doi:10.1080/03610927408827101>,
HUBERT, L. (1974) <doi:10.1080/01621459.1974.10480191>,
TIBSHIRANI, R., WALTHER, G., HASTIE, T. (2001) <doi:10.1111/1467-9868.00293>,
BRECKENRIDGE, J.N. (2000) <doi:10.1207/S15327906MBR3502_5>,
WALESIAK, M., DUDEK, A. (2008) <doi:10.1007/978-3-540-78246-9_11>).
Author: Marek Walesiak <marek.walesiak@ue.wroc.pl>, Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Maintainer: Andrzej Dudek <andrzej.dudek@ue.wroc.pl>
Diff between clusterSim versions 0.47-3 dated 2018-11-28 and 0.47-4 dated 2019-05-24
DESCRIPTION | 11 +++++------ MD5 | 8 ++++---- NAMESPACE | 1 - R/cluster.Description.r | 28 ++++++++++++++++++++++++++-- R/cluster.Sim.r | 2 +- 5 files changed, 36 insertions(+), 14 deletions(-)
Title: Wavelet Scalogram Tools for Time Series Analysis
Description: Provides scalogram based wavelet tools for time series analysis: wavelet power spectrum, scalogram, windowed scalogram, windowed scalogram difference (see Bolos et al. (2017) <doi:10.1016/j.amc.2017.05.046>), scale index and windowed scale index (Benitez et al. (2010) <doi:10.1016/j.camwa.2010.05.010>).
Author: Vicente J. Bolos and Rafael Benitez
Maintainer: Vicente J. Bolos <vicente.bolos@uv.es>
Diff between wavScalogram versions 0.1.0 dated 2019-03-06 and 1.0.0 dated 2019-05-24
DESCRIPTION | 8 +- MD5 | 34 +++++---- NAMESPACE | 1 R/cwt_wst.R | 131 ++++++++++++++++++++---------------- R/fourier_factor.R |only R/pow2scales.R | 5 + R/scale_index.R | 72 ++++++++++++-------- R/scalogram.R | 56 +++++++++------ R/wavelet_radius.R | 2 R/windowed_scale_index.R | 103 ++++++++++++++++------------ R/windowed_scalogram.R | 64 ++++++++++------- R/wsd.R | 158 +++++++++++++++++++++++++++----------------- man/cwt_wst.Rd | 20 ++++- man/fourier_factor.Rd |only man/scale_index.Rd | 29 +++++--- man/scalogram.Rd | 20 ++++- man/windowed_scale_index.Rd | 35 ++++++--- man/windowed_scalogram.Rd | 23 ++++-- man/wsd.Rd | 40 ++++++++--- 19 files changed, 501 insertions(+), 300 deletions(-)
Title: Stepwise Regression Analysis
Description: Stepwise regression analysis for variable selection can be used to get the best candidate final regression model in univariate or multivariate regression analysis with the 'forward' and 'stepwise' steps. Procedure uses Akaike information criterion, the small-sample-size corrected version of Akaike information criterion, Bayesian information criterion, Hannan and Quinn information criterion, the corrected form of Hannan and Quinn information criterion, Schwarz criterion and significance levels as selection criteria, where the significance levels for entry and for stay are set to 0.15 as default. Multicollinearity detection in regression model are performed by checking tolerance value, which is set to 1e-7 as default. Continuous variables nested within class effect and weighted stepwise regression are also considered in this package.
Author: Junhui Li,Kun Cheng,Wenxin Liu
Maintainer: Junhui Li <junhuili@cau.edu.cn>
Diff between StepReg versions 1.0.1 dated 2019-01-17 and 1.1.0 dated 2019-05-24
DESCRIPTION | 10 +++++----- MD5 | 8 ++++---- R/stepwise.R | 43 +++++++++++++++++++++++++++++++++---------- man/StepReg-package.Rd | 6 +++--- man/stepwise.Rd | 29 ++++++++++++++++++----------- 5 files changed, 63 insertions(+), 33 deletions(-)
Title: Stochastic Complexity-Based Conditional Independence Test for
Discrete Data
Description: An efficient implementation of SCCI using 'Rcpp'. SCCI is short for the Stochastic Complexity-based Conditional Independence criterium (Marx and Vreeken, 2019). SCCI is an asymptotically unbiased and L2 consistent estimator of (conditional) mutual information for discrete data.
Author: Alexander Marx [aut,cre] Jilles Vreeken [aut]
Maintainer: Alexander Marx <amarx@mpi-inf.mpg.de>
Diff between SCCI versions 1.0 dated 2019-03-01 and 1.1 dated 2019-05-24
DESCRIPTION | 8 ++++---- MD5 | 6 +++--- inst/CITATION | 1 + src/core.cpp | 4 ++-- 4 files changed, 10 insertions(+), 9 deletions(-)
Title: Adaptive Rejection Metropolis Sampling (ARMS) via 'Rcpp'
Description: An efficient 'Rcpp' implementation of the Adaptive Rejection Metropolis Sampling (ARMS) algorithm proposed by Gilks, W. R., Best, N. G. and Tan, K. K. C. (1995) <doi:10.2307/2986138>. This allows for sampling from a univariate target probability distribution specified by its (potentially unnormalised) log density.
Author: Michael Bertolacci [aut, cre]
Maintainer: Michael Bertolacci <m.bertolacci@gmail.com>
Diff between armspp versions 0.0.1 dated 2019-04-04 and 0.0.2 dated 2019-05-24
DESCRIPTION | 10 +++++----- MD5 | 17 +++++++++-------- NAMESPACE | 1 - NEWS.md | 4 ++++ R/armspp.R | 1 - build/vignette.rds |binary inst/doc/arms.html | 24 +++++++++++------------- src/arms-gibbs.cpp | 8 ++++---- src/progress.h |only tests/testthat/test-arms-gibbs.R | 21 ++++++++++++--------- 10 files changed, 45 insertions(+), 41 deletions(-)
Title: Extended Structural Equation Modelling
Description: Create structural equation models that can be manipulated programmatically.
Models may be specified with matrices or paths (LISREL or RAM)
Example models include confirmatory factor, multiple group, mixture
distribution, categorical threshold, modern test theory, differential
Fit functions include full information maximum likelihood, maximum likelihood, and weighted least squares.
equations, state space, and many others.
Support and advanced package binaries available at <http://openmx.ssri.psu.edu>.
The software is described in Neale, Hunter, Pritikin, Zahery, Brick,
Kirkpatrick, Estabrook, Bates, Maes, & Boker (2016) <doi:10.1007/s11336-014-9435-8>.
Author: Steven M. Boker [aut],
Michael C. Neale [aut],
Hermine H. Maes [aut],
Michael J. Wilde [ctb],
Michael Spiegel [aut],
Timothy R. Brick [aut],
Ryne Estabrook [aut],
Timothy C. Bates [aut],
Paras Mehta [ctb],
Timo von Oertzen [ctb],
Ross J. Gore [aut],
Michael D. Hunter [aut],
Daniel C. Hackett [ctb],
Julian Karch [ctb],
Andreas M. Brandmaier [ctb],
Joshua N. Pritikin [aut, cre],
Mahsa Zahery [aut],
Robert M. Kirkpatrick [aut],
Yang Wang [ctb],
Charles Driver [ctb],
Massachusetts Institute of Technology [cph],
S. G. Johnson [cph],
Association for Computing Machinery [cph],
Dieter Kraft [cph],
Stefan Wilhelm [cph],
Sarah Medland [cph],
Carl F. Falk [cph],
Matt Keller [cph],
Manjunath B G [cph],
The Regents of the University of California [cph],
Lester Ingber [cph],
Wong Shao Voon [cph],
Juan Palacios [cph],
Jiang Yang [cph],
Gavin Band [cph],
Yann Collet [cph],
Facebook, Inc. [cph],
Yuta Mori [cph],
Shaun Purcell [cph],
Christopher Chang [cph]
Maintainer: Joshua N. Pritikin <jpritikin@pobox.com>
Diff between OpenMx versions 2.12.2 dated 2019-02-08 and 2.13.0 dated 2019-05-24
OpenMx-2.12.2/OpenMx/NEWS |only OpenMx-2.12.2/OpenMx/data/HS.fake.data.txt.gz |only OpenMx-2.12.2/OpenMx/inst/models/nightly/data/jointdata.txt |only OpenMx-2.12.2/OpenMx/inst/models/passing/MxTryHardTest.R |only OpenMx-2.12.2/OpenMx/inst/models/passing/SimpleMix.R |only OpenMx-2.12.2/OpenMx/inst/models/passing/data/jointdata.txt |only OpenMx-2.12.2/OpenMx/inst/models/passing/data/lazarsfeld.ord |only OpenMx-2.12.2/OpenMx/inst/models/passing/loadData.R |only OpenMx-2.12.2/OpenMx/man/imxJiggle.Rd |only OpenMx-2.12.2/OpenMx/src/subnp.cpp |only OpenMx-2.13.0/OpenMx/DESCRIPTION | 53 OpenMx-2.13.0/OpenMx/MD5 | 531 +-- OpenMx-2.13.0/OpenMx/NAMESPACE | 3 OpenMx-2.13.0/OpenMx/NEWS.md | 52 OpenMx-2.13.0/OpenMx/R/0ClassUnion.R | 4 OpenMx-2.13.0/OpenMx/R/MxAlgebra.R | 40 OpenMx-2.13.0/OpenMx/R/MxAlgebraConvert.R | 4 OpenMx-2.13.0/OpenMx/R/MxAutoStart.R | 65 OpenMx-2.13.0/OpenMx/R/MxCompute.R | 333 + OpenMx-2.13.0/OpenMx/R/MxData.R | 186 - OpenMx-2.13.0/OpenMx/R/MxDataWLS.R | 15 OpenMx-2.13.0/OpenMx/R/MxExpectation.R | 2 OpenMx-2.13.0/OpenMx/R/MxExpectationBA81.R | 1 OpenMx-2.13.0/OpenMx/R/MxExpectationGREML.R | 2 OpenMx-2.13.0/OpenMx/R/MxExpectationLISREL.R | 5 OpenMx-2.13.0/OpenMx/R/MxExpectationNormal.R | 22 OpenMx-2.13.0/OpenMx/R/MxFactorScores.R | 89 OpenMx-2.13.0/OpenMx/R/MxFitFunctionWLS.R | 96 OpenMx-2.13.0/OpenMx/R/MxLISRELModel.R | 6 OpenMx-2.13.0/OpenMx/R/MxMI.R | 1 OpenMx-2.13.0/OpenMx/R/MxMMI.R | 82 OpenMx-2.13.0/OpenMx/R/MxModel.R | 17 OpenMx-2.13.0/OpenMx/R/MxModelFunctions.R | 10 OpenMx-2.13.0/OpenMx/R/MxModelParameters.R | 6 OpenMx-2.13.0/OpenMx/R/MxMultiModel.R | 20 OpenMx-2.13.0/OpenMx/R/MxNamespace.R | 36 OpenMx-2.13.0/OpenMx/R/MxOptions.R | 22 OpenMx-2.13.0/OpenMx/R/MxPath.R | 10 OpenMx-2.13.0/OpenMx/R/MxRAMModel.R | 11 OpenMx-2.13.0/OpenMx/R/MxRobustSE.R | 32 OpenMx-2.13.0/OpenMx/R/MxRun.R | 33 OpenMx-2.13.0/OpenMx/R/MxRunHelperFunctions.R | 113 OpenMx-2.13.0/OpenMx/R/MxSE.R | 89 OpenMx-2.13.0/OpenMx/R/MxSaturatedModel.R | 9 OpenMx-2.13.0/OpenMx/R/MxSummary.R | 66 OpenMx-2.13.0/OpenMx/R/MxTryHard.R | 129 OpenMx-2.13.0/OpenMx/R/MxUnitTesting.R | 8 OpenMx-2.13.0/OpenMx/R/MxVersion.R | 2 OpenMx-2.13.0/OpenMx/R/omxReadGRMBin.R |only OpenMx-2.13.0/OpenMx/R/sysdata.rda |binary OpenMx-2.13.0/OpenMx/R/zzz.R | 41 OpenMx-2.13.0/OpenMx/README.md | 43 OpenMx-2.13.0/OpenMx/configure | 3 OpenMx-2.13.0/OpenMx/data/Oscillator.txt.gz |only OpenMx-2.13.0/OpenMx/data/datalist | 3 OpenMx-2.13.0/OpenMx/data/lazarsfeld.csv.gz |only OpenMx-2.13.0/OpenMx/demo/00Index | 1 OpenMx-2.13.0/OpenMx/demo/BivariateHeterogeneity_MatrixRaw.R | 2 OpenMx-2.13.0/OpenMx/demo/BivariateHeterogeneity_PathRaw.R | 2 OpenMx-2.13.0/OpenMx/demo/LDE.R |only OpenMx-2.13.0/OpenMx/demo/UnivariateTwinAnalysis_MatrixRaw.R | 2 OpenMx-2.13.0/OpenMx/inst/CITATION | 16 OpenMx-2.13.0/OpenMx/inst/models/codeRed/fail_on_re-run_entity_already_exists.R | 10 OpenMx-2.13.0/OpenMx/inst/models/codeRed/umxACE_codeRed.R | 8 OpenMx-2.13.0/OpenMx/inst/models/enormous/ifa-cyh2011-sim1.R | 4 OpenMx-2.13.0/OpenMx/inst/models/failing/SimpleConfidenceIntervals.R | 17 OpenMx-2.13.0/OpenMx/inst/models/failing/mice.R | 15 OpenMx-2.13.0/OpenMx/inst/models/nightly/180209--defvars.R | 7 OpenMx-2.13.0/OpenMx/inst/models/nightly/CSOLNP_segfault_regression_test--unidentifed_EFA.R |only OpenMx-2.13.0/OpenMx/inst/models/nightly/ETC88.R | 1 OpenMx-2.13.0/OpenMx/inst/models/nightly/FactorScores.R | 28 OpenMx-2.13.0/OpenMx/inst/models/nightly/GrowthMixtureModelRandomStarts.R | 6 OpenMx-2.13.0/OpenMx/inst/models/nightly/LegacyWLS+CI.R | 48 OpenMx-2.13.0/OpenMx/inst/models/nightly/ModelIdentification.R | 15 OpenMx-2.13.0/OpenMx/inst/models/nightly/MultigroupRobustSE_test.R | 2 OpenMx-2.13.0/OpenMx/inst/models/nightly/MxTryHardTest.R |only OpenMx-2.13.0/OpenMx/inst/models/nightly/SimpleMix.R |only OpenMx-2.13.0/OpenMx/inst/models/nightly/SkippedRows.R | 2 OpenMx-2.13.0/OpenMx/inst/models/nightly/StateSpaceContinuous.R | 79 OpenMx-2.13.0/OpenMx/inst/models/nightly/StateSpaceLatentGrowth.R | 17 OpenMx-2.13.0/OpenMx/inst/models/nightly/brooke.R | 8 OpenMx-2.13.0/OpenMx/inst/models/nightly/ifa-2d-mg.R | 3 OpenMx-2.13.0/OpenMx/inst/models/nightly/ifa-cai2009.R | 10 OpenMx-2.13.0/OpenMx/inst/models/nightly/mplus-ex9.11.R | 1 OpenMx-2.13.0/OpenMx/inst/models/nightly/mplus-ex9.6.R | 4 OpenMx-2.13.0/OpenMx/inst/models/nightly/testPolychoricMatrix.R |only OpenMx-2.13.0/OpenMx/inst/models/nightly/thresholdModel1Factor5VariateWLS.R | 18 OpenMx-2.13.0/OpenMx/inst/models/passing/ACEDuplicateMatrices.R | 61 OpenMx-2.13.0/OpenMx/inst/models/passing/ACELRTCI20160808.R | 2 OpenMx-2.13.0/OpenMx/inst/models/passing/AnalyticConstraintJacobians--Eq_and_Ineq.R | 60 OpenMx-2.13.0/OpenMx/inst/models/passing/Autoregressive_Tree_Matrix.R | 1 OpenMx-2.13.0/OpenMx/inst/models/passing/Autoregressive_Tree_Path.R | 1 OpenMx-2.13.0/OpenMx/inst/models/passing/BivRegStdTestSE.R | 3 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OpenMx-2.13.0/OpenMx/src/entropy_common.c |only OpenMx-2.13.0/OpenMx/src/finiteDifferences.h | 16 OpenMx-2.13.0/OpenMx/src/fitMultigroup.cpp | 24 OpenMx-2.13.0/OpenMx/src/fse_compress.c |only OpenMx-2.13.0/OpenMx/src/fse_decompress.c |only OpenMx-2.13.0/OpenMx/src/glue.cpp | 67 OpenMx-2.13.0/OpenMx/src/glue.h | 4 OpenMx-2.13.0/OpenMx/src/huf_compress.c |only OpenMx-2.13.0/OpenMx/src/huf_decompress.c |only OpenMx-2.13.0/OpenMx/src/include |only OpenMx-2.13.0/OpenMx/src/matlogexp.cpp |only OpenMx-2.13.0/OpenMx/src/matrix.cpp | 40 OpenMx-2.13.0/OpenMx/src/matrix.h | 4 OpenMx-2.13.0/OpenMx/src/minicsv.h | 2 OpenMx-2.13.0/OpenMx/src/omxAlgebra.cpp | 59 OpenMx-2.13.0/OpenMx/src/omxAlgebra.h | 4 OpenMx-2.13.0/OpenMx/src/omxAlgebraFitFunction.cpp | 12 OpenMx-2.13.0/OpenMx/src/omxBVN.h | 13 OpenMx-2.13.0/OpenMx/src/omxData.cpp | 1138 ++++-- OpenMx-2.13.0/OpenMx/src/omxData.h | 81 OpenMx-2.13.0/OpenMx/src/omxDefines.h | 26 OpenMx-2.13.0/OpenMx/src/omxExpectation.cpp | 40 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OpenMx-2.13.0/OpenMx/src/omxRowFitFunction.cpp | 14 OpenMx-2.13.0/OpenMx/src/omxSadmvnWrapper.h | 8 OpenMx-2.13.0/OpenMx/src/omxState.cpp | 147 OpenMx-2.13.0/OpenMx/src/omxState.h | 56 OpenMx-2.13.0/OpenMx/src/omxStateSpaceExpectation.cpp | 2 OpenMx-2.13.0/OpenMx/src/omxWLSFitFunction.cpp | 60 OpenMx-2.13.0/OpenMx/src/pgenlib_internal.cpp |only OpenMx-2.13.0/OpenMx/src/pgenlib_internal.h |only OpenMx-2.13.0/OpenMx/src/plink2_base.cc |only OpenMx-2.13.0/OpenMx/src/plink2_base.h |only OpenMx-2.13.0/OpenMx/src/sqlite3.c |only OpenMx-2.13.0/OpenMx/src/ssMLFit.cpp | 2 OpenMx-2.13.0/OpenMx/src/xxhash.c |only OpenMx-2.13.0/OpenMx/src/zbuff_compress.c |only OpenMx-2.13.0/OpenMx/src/zbuff_decompress.c |only OpenMx-2.13.0/OpenMx/src/zstd_common.c |only OpenMx-2.13.0/OpenMx/src/zstd_compress.c |only OpenMx-2.13.0/OpenMx/src/zstd_decompress.c |only 280 files changed, 6767 insertions(+), 3144 deletions(-)
Title: Software for Project AERO
Description: Implements methods for anticipating the emergence and eradication
of infectious diseases from surveillance time series. Also provides support
for computational experiments testing the performance of such methods.
Author: Eamon O'Dea [aut, cre]
Maintainer: Eamon O'Dea <odea35@gmail.com>
Diff between spaero versions 0.4.0 dated 2018-12-16 and 0.5.0 dated 2019-05-24
DESCRIPTION | 8 ++-- MD5 | 18 +++++----- NEWS.md | 6 ++- R/simulation.R | 64 +++++++++++++++++++++++--------------- build/vignette.rds |binary inst/doc/spaero-introduction.Rmd | 31 ++++++++++-------- inst/doc/spaero-introduction.pdf |binary tests/testthat/test-simulator.R | 63 +++++++++++++++++++++++++++---------- tests/testthat/test-stats.R | 19 ++++++++++- vignettes/spaero-introduction.Rmd | 31 ++++++++++-------- 10 files changed, 158 insertions(+), 82 deletions(-)
Title: Restricted Statistical Estimation and Inference for Linear
Models
Description: Allow for easy-to-use testing or evaluating of linear equality and inequality
restrictions about parameters and effects in (generalized) linear statistical models.
Author: Leonard Vanbrabant [aut, cre],
Yves Rosseel [ctb]
Maintainer: Leonard Vanbrabant <Leonard.Vanbrabant@Ugent.be>
Diff between restriktor versions 0.1-80.911 dated 2018-10-31 and 0.2-15 dated 2019-05-24
DESCRIPTION | 6 MD5 | 126 +- NAMESPACE | 171 +-- R/Gaussian_Elimination.R | 114 +- R/conGLM.R | 712 +++++++------- R/conGLM_fit.R | 490 ++++----- R/conLM.R | 709 ++++++-------- R/conMLM.R | 688 ++++++------- R/conRLM.R | 786 +++++++-------- R/conRLM_fit.R | 404 +++---- R/conRLM_tests_F_Wald_score.R | 302 ++--- R/conTest.R | 254 ++--- R/conTest_ceq_conGLM_F_Wald_score.R | 316 +++--- R/conTest_ceq_conLM_F_Wald_score.R | 374 +++---- R/conTest_ceq_conRLM_F_Wald_score.R | 292 ++--- R/conTest_conGLM.R | 1504 ++++++++++++++--------------- R/conTest_conLM.R | 1822 ++++++++++++++++++------------------ R/conTest_conMLM.R | 512 +++++----- R/conTest_conRLM.R | 1582 +++++++++++++++---------------- R/conTest_print.R | 484 ++++----- R/conTest_summary.R | 70 - R/con_augmented_information.R | 202 +-- R/con_boot.R | 48 R/con_boot_data.R | 30 R/con_boot_fixed.R | 28 R/con_constraints.R | 243 ++-- R/con_goric.R | 1016 ++++++++++++++------ R/con_gorica_est.R |only R/con_gorica_est_summary.R |only R/con_iht.R | 4 R/con_loglik.R | 86 - R/con_partable.R | 179 ++- R/con_pbar.R | 50 R/con_pvalue.R | 876 ++++++++--------- R/con_sandwich.R | 446 ++++---- R/con_solver.R | 302 +++-- R/con_weights.R | 226 ++-- R/restriktor.R | 76 - R/restriktor_print.R | 123 +- R/restriktor_print_summary.R | 222 ++-- R/restriktor_summary.R | 416 ++++---- R/utilities.R | 198 +-- R/zzz.R | 14 README | 6 inst/NEWS | 90 - man/AngerManagement.Rd | 62 - man/Burns.Rd | 64 - man/ConTest.Rd | 702 ++++++------- man/ConTestC.Rd | 232 ++-- man/ConTestLRT.Rd | 624 ++++++------ man/ConTestScore.Rd | 640 ++++++------ man/ConTestWald.Rd | 616 ++++++------ man/Exam.Rd | 52 - man/Hurricanes.Rd | 54 - man/ZelazoKolb1972.Rd | 60 - man/conTestF.Rd | 666 ++++++------- man/conTest_ceq.Rd | 332 +++--- man/conTest_methods.Rd | 84 - man/conTest_summary.Rd | 310 +++--- man/goric.Rd | 277 +++-- man/mixingWeights.Rd | 152 +-- man/restriktor-package.rd | 308 +++--- man/restriktor.Rd | 824 ++++++++-------- man/restriktor_methods.Rd | 218 ++-- tests/testCases.R | 84 - 65 files changed, 11821 insertions(+), 11139 deletions(-)
Title: Extract Remote Sensing Vegetation Phenology
Description: The merits of 'TIMESAT' and 'phenopix' are adopted. Besides, a simple and
growing season dividing method and a practical snow elimination method
based on Whittaker were proposed. 7 curve fitting methods and 4 phenology
extraction methods were provided. Parameters boundary are considered for
every curve fitting methods according to their ecological meaning.
And 'optimx' is used to select best optimization method for different
curve fitting methods.
Reference:
Dongdong Kong, R package: A state-of-the-art Vegetation Phenology extraction package,
phenofit version 0.2.3, <https://github.com/kongdd/phenofit>;
Zhang, Q., Kong, D., Shi, P., Singh, V.P., Sun, P., 2018. Vegetation phenology
on the Qinghai-Tibetan Plateau and its response to climate change (1982–2013).
Agric. For. Meteorol. 248, 408–417. <doi:10.1016/j.agrformet.2017.10.026>.
Author: Dongdong Kong [aut, cre],
Mingzhong Xiao [aut],
Yongqiang Zhang [aut],
Xihui Gu [aut],
Jianjian Cui [aut]
Maintainer: Dongdong Kong <kongdd.sysu@gmail.com>
Diff between phenofit versions 0.2.3 dated 2019-05-23 and 0.2.4 dated 2019-05-24
DESCRIPTION | 12 +++++++++--- MD5 | 2 +- 2 files changed, 10 insertions(+), 4 deletions(-)
Title: Bivariate Probability Distributions
Description: Contains convenience functions for constructing, plotting and evaluating bivariate probability distributions, including their probability mass functions, probability density functions and cumulative distribution functions. Supports uniform (discrete and continuous), binomial, Poisson, categorical, normal, bimodal and Dirichlet (trivariate) distributions, and kernel smoothing and empirical cumulative distribution functions.
Author: Abby Spurdle
Maintainer: Abby Spurdle <spurdle.a@gmail.com>
Diff between bivariate versions 0.3.1 dated 2019-02-27 and 0.4.1 dated 2019-05-24
bivariate-0.3.1/bivariate/R/plot2d.r |only bivariate-0.3.1/bivariate/R/returned_functions.r |only bivariate-0.3.1/bivariate/man/bimodal.Rd |only bivariate-0.3.1/bivariate/man/binomial.Rd |only bivariate-0.3.1/bivariate/man/kernel.Rd |only bivariate-0.3.1/bivariate/man/methods.Rd |only bivariate-0.3.1/bivariate/man/normal.Rd |only bivariate-0.3.1/bivariate/man/poisson.Rd |only bivariate-0.3.1/bivariate/man/returned_functions.Rd |only bivariate-0.3.1/bivariate/man/uniform.Rd |only bivariate-0.4.1/bivariate/DESCRIPTION | 18 bivariate-0.4.1/bivariate/MD5 | 54 +- bivariate-0.4.1/bivariate/NAMESPACE | 15 bivariate-0.4.1/bivariate/R/bimodal.r | 153 +++---- bivariate-0.4.1/bivariate/R/binomial.r | 73 +-- bivariate-0.4.1/bivariate/R/bv.r |only bivariate-0.4.1/bivariate/R/bv_other.r |only bivariate-0.4.1/bivariate/R/categorical.r |only bivariate-0.4.1/bivariate/R/cu.r | 108 ++--- bivariate-0.4.1/bivariate/R/dirichlet.r |only bivariate-0.4.1/bivariate/R/du.r | 67 +-- bivariate-0.4.1/bivariate/R/empirical.r |only bivariate-0.4.1/bivariate/R/kernel.r | 114 ----- bivariate-0.4.1/bivariate/R/normal.r | 104 ++--- bivariate-0.4.1/bivariate/R/poisson.r | 100 ++--- bivariate-0.4.1/bivariate/inst/doc/bivariate.R | 232 +++++++---- bivariate-0.4.1/bivariate/inst/doc/bivariate.Rnw | 373 +++++++++++-------- bivariate-0.4.1/bivariate/inst/doc/bivariate.pdf |binary bivariate-0.4.1/bivariate/man/rd_01_uniform.Rd |only bivariate-0.4.1/bivariate/man/rd_02_binomial.Rd |only bivariate-0.4.1/bivariate/man/rd_03_poisson.Rd |only bivariate-0.4.1/bivariate/man/rd_04_categorical.Rd |only bivariate-0.4.1/bivariate/man/rd_05_normal.Rd |only bivariate-0.4.1/bivariate/man/rd_06_bimodal.Rd |only bivariate-0.4.1/bivariate/man/rd_07_dirichlet.Rd |only bivariate-0.4.1/bivariate/man/rd_08_nonparametric.Rd |only bivariate-0.4.1/bivariate/man/rd_09_print_method.Rd |only bivariate-0.4.1/bivariate/man/rd_10_plot_methods.Rd |only bivariate-0.4.1/bivariate/man/rd_11_theme.Rd |only bivariate-0.4.1/bivariate/vignettes/Makefile | 4 bivariate-0.4.1/bivariate/vignettes/bivariate.Rnw | 373 +++++++++++-------- 41 files changed, 937 insertions(+), 851 deletions(-)
Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides:
'%.>%' dot-pipe (an 'S3' configurable pipe),
'let()'
(converts non-standard evaluation interfaces to parametric standard
evaluation interfaces, inspired by 'gtools:strmacro()' and 'base::bquote()'),
'build_frame()'/'draw_frame()' ('data.frame' example tools),
'qc()' (quoting concatenate),
':=' (named map builder),
and more.
Author: John Mount [aut, cre],
Nina Zumel [aut],
Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>
Diff between wrapr versions 1.8.6 dated 2019-04-02 and 1.8.7 dated 2019-05-24
DESCRIPTION | 10 MD5 | 55 ++- NAMESPACE | 4 NEWS.md | 5 R/as_dot_fn.R | 26 + R/cf.R | 7 R/string_interpolation.R | 50 +-- README.md | 276 +++++++++++++------ build/vignette.rds |binary inst/doc/CornerCases.html | 401 +++++++++++++++++++++------ inst/doc/DebugFnW.html | 387 ++++++++++++++++++++------ inst/doc/FrameTools.html | 371 ++++++++++++++++++++----- inst/doc/Function_Objects.html | 411 +++++++++++++++++++++------- inst/doc/Named_Arguments.html | 337 +++++++++++++++++++---- inst/doc/QuotingConcatinate.html | 319 ++++++++++++++++++---- inst/doc/SubstitutionModes.html | 365 ++++++++++++++++++++----- inst/doc/bquote.Rmd | 2 inst/doc/bquote.html | 369 ++++++++++++++++++++----- inst/doc/dot_pipe.html | 303 +++++++++++++++++---- inst/doc/lambda.html | 305 +++++++++++++++++---- inst/doc/let.html | 339 +++++++++++++++++++---- inst/doc/named_map_builder.html | 309 ++++++++++++++++++--- inst/doc/wrapr_applicable.html | 475 +++++++++++++++++++++++---------- inst/unit_tests/test_dot_quote.R |only inst/unit_tests/test_pipe_quote_name.R |only inst/unit_tests/test_qchar_frame.R |only inst/unit_tests/test_str_stuff.R | 14 man/qchar_frame.Rd | 3 man/sinterp.Rd | 8 vignettes/bquote.Rmd | 2 30 files changed, 4025 insertions(+), 1128 deletions(-)
Title: Interface for the RobinHood.com No Commission Investing Platform
Description: Execute API calls to the RobinHood <https://robinhood.com> investing platform. Functionality includes accessing account data and current holdings, retrieving investment statistics and quotes, placing and canceling orders, getting market trading hours, searching investments by popular tag, and interacting with watch lists.
Author: Joseph Blubaugh
Maintainer: Joseph Blubaugh <jestonblu@gmail.com>
Diff between RobinHood versions 1.0.5 dated 2019-04-06 and 1.0.7 dated 2019-05-24
DESCRIPTION | 10 ++--- MD5 | 80 ++++++++++++++++++++++----------------------- NAMESPACE | 18 ++++++++++ R/RobinHood.R | 2 - R/api_accounts.R | 15 ++++---- R/api_endpoints.R | 1 R/api_fundamentals.R | 37 ++++++++++++-------- R/api_historicals.R | 13 +++++-- R/api_instruments.R | 7 ++- R/api_login.R | 13 ++----- R/api_logout.R | 3 + R/api_markets.R | 15 ++++---- R/api_option_instruments.R | 8 ++-- R/api_option_positions.R | 5 +- R/api_orders.R | 17 +++++---- R/api_portfolio.R | 75 +++++++++++++++++++++++++++--------------- R/api_positions.R | 9 ++--- R/api_quote.R | 9 ++--- R/api_tag.R | 5 +- R/api_tickers.R | 11 +++--- R/api_user.R | 5 +- R/api_watchlist.R | 7 ++- R/cancel_order.R | 2 - R/get_accounts.R | 2 - R/get_fundamentals.R | 41 ++++++++++++++++++++--- R/get_historicals.R | 2 - R/get_market_hours.R | 10 ++--- R/get_order_history.R | 4 +- R/get_order_status.R | 2 - R/get_portfolios.R | 41 ++++++++++++++++++++--- R/get_positions.R | 9 ++--- R/get_quote.R | 4 +- R/get_tag.R | 2 - R/get_tickers.R | 35 ++++++++++++++++++- R/get_user.R | 4 +- R/logout.R | 2 - R/place_order.R | 2 - R/watchlist.R | 2 - man/api_portfolios.Rd | 4 +- man/get_portfolios.Rd | 11 ++++-- man/get_tickers.Rd | 4 +- 41 files changed, 357 insertions(+), 191 deletions(-)
Title: Multiple Locus Association Mapping on a Genome-Wide Scale
Description: An implementation of multiple-locus association mapping on a genome-wide scale. 'Eagle' can handle inbred and outbred study populations, populations of arbitrary unknown complexity, and data larger than the memory capacity of the computer. Since 'Eagle' is based on linear mixed models, it is best suited to the analysis of data on continuous traits. However, it can tolerate non-normal data. 'Eagle' reports, as its findings, the best set of snp in strongest association with a trait. For users unfamiliar with R, to perform an analysis, run 'OpenGUI()'. This opens a web browser to the menu-driven user interface for the input of data, and for performing genome-wide analysis.
Author: Andrew George [aut, cre],
Joshua Bowden [ctb],
Ryan Stephenson [ctb],
Hyun Kang [ctb],
Noah Zaitlen [ctb],
Claire Wade [ctb],
Andrew Kirby [ctb],
David Heckerman [ctb],
Mark Daly [ctb],
Eleazar Eskin [ctb]
Maintainer: Andrew George <andrew.george@csiro.au>
Diff between Eagle versions 1.5.0 dated 2019-05-17 and 1.5.1 dated 2019-05-24
DESCRIPTION | 12 ++--- MD5 | 8 +-- NAMESPACE | 6 ++ R/onAttach.R | 2 inst/shiny_app/app.R | 122 ++++++++++++++++++++++++++++----------------------- 5 files changed, 83 insertions(+), 67 deletions(-)
Title: 'DataRobot' Predictive Modeling API
Description: For working with the 'DataRobot' predictive modeling platform's API <https://www.datarobot.com/>.
Author: Ron Pearson [aut], Zachary Deane-Mayer [aut], David Chudzicki [aut], Dallin Akagi [aut], Sergey Yurgenson [aut], Thakur Raj Anand [aut], Peter Hurford [aut]
Maintainer: Peter Hurford <api-maintainer@datarobot.com>
Diff between datarobot versions 2.12.1 dated 2019-02-27 and 2.13.0 dated 2019-05-24
datarobot-2.12.1/datarobot/R/CreateFeaturelist.R |only datarobot-2.12.1/datarobot/R/GetFeaturelist.R |only datarobot-2.12.1/datarobot/inst/doc/ReasonCodeVignette.R |only datarobot-2.12.1/datarobot/inst/doc/ReasonCodeVignette.Rmd |only datarobot-2.12.1/datarobot/inst/doc/ReasonCodeVignette.html |only datarobot-2.12.1/datarobot/vignettes/ReasonCodeVignette.Rmd |only datarobot-2.12.1/datarobot/vignettes/reasonCodeAsDataFrameTopBottom.rds |only datarobot-2.12.1/datarobot/vignettes/reasonCodeAsDataFrameWithExposure.rds |only datarobot-2.12.1/datarobot/vignettes/results.rds |only datarobot-2.12.1/datarobot/vignettes/testPredictions.rds |only datarobot-2.13.0/datarobot/DESCRIPTION | 12 datarobot-2.13.0/datarobot/MD5 | 265 +++++----- datarobot-2.13.0/datarobot/NAMESPACE | 40 + datarobot-2.13.0/datarobot/NEWS | 57 ++ datarobot-2.13.0/datarobot/R/AdvancedTuning.R |only datarobot-2.13.0/datarobot/R/Blenders.R | 27 + datarobot-2.13.0/datarobot/R/ConnectToDataRobot.R | 3 datarobot-2.13.0/datarobot/R/DataRobotRequests.R | 2 datarobot-2.13.0/datarobot/R/DeletePredictJob.R | 2 datarobot-2.13.0/datarobot/R/Enums.R | 89 +-- datarobot-2.13.0/datarobot/R/FeatureImpact.R | 72 ++ datarobot-2.13.0/datarobot/R/Featurelists.R |only datarobot-2.13.0/datarobot/R/Features.R | 10 datarobot-2.13.0/datarobot/R/GetPredictions.R | 215 ++++++-- datarobot-2.13.0/datarobot/R/Jobs.R | 47 - datarobot-2.13.0/datarobot/R/ListFeaturelists.R | 78 -- datarobot-2.13.0/datarobot/R/ListModelJobs.R | 31 - datarobot-2.13.0/datarobot/R/Models.R | 179 +++++- datarobot-2.13.0/datarobot/R/MultiSeries.R | 32 + datarobot-2.13.0/datarobot/R/ParetoFront.R |only datarobot-2.13.0/datarobot/R/Partitions.R | 59 +- datarobot-2.13.0/datarobot/R/PredictionDatasets.R | 48 + datarobot-2.13.0/datarobot/R/PredictionExplanations.R |only datarobot-2.13.0/datarobot/R/Projects.R | 2 datarobot-2.13.0/datarobot/R/ReasonCodes.R | 97 ++- datarobot-2.13.0/datarobot/R/SetupProject.R | 1 datarobot-2.13.0/datarobot/R/StarredModels.R |only datarobot-2.13.0/datarobot/R/StartAutopilot.R | 40 + datarobot-2.13.0/datarobot/R/TestUtilities.R | 2 datarobot-2.13.0/datarobot/R/TrainingPredictions.R | 31 + datarobot-2.13.0/datarobot/build/vignette.rds |binary datarobot-2.13.0/datarobot/inst/doc/AdvancedTuning.R |only datarobot-2.13.0/datarobot/inst/doc/AdvancedTuning.Rmd |only datarobot-2.13.0/datarobot/inst/doc/AdvancedTuning.html |only datarobot-2.13.0/datarobot/inst/doc/AdvancedVignette.html | 2 datarobot-2.13.0/datarobot/inst/doc/DatetimePartitionedProjects.R | 4 datarobot-2.13.0/datarobot/inst/doc/DatetimePartitionedProjects.Rmd | 4 datarobot-2.13.0/datarobot/inst/doc/DatetimePartitionedProjects.html | 4 datarobot-2.13.0/datarobot/inst/doc/IntroductionToDataRobot.R | 7 datarobot-2.13.0/datarobot/inst/doc/IntroductionToDataRobot.Rmd | 15 datarobot-2.13.0/datarobot/inst/doc/IntroductionToDataRobot.html | 17 datarobot-2.13.0/datarobot/inst/doc/Multiclass.R | 6 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