Wed, 19 Dec 2018

Package umx updated to version 2.9.0 with previous version 2.8.5 dated 2018-10-06

Title: Structural Equation and Twin Modeling in R
Description: Quickly create, run, and report structural equation and twin models. See '?umx' for help, and file.show(system.file("NEWS", package="umx")) for NEWS.
Author: Timothy C Bates [aut, cre] (<https://orcid.org/0000-0002-1153-9007>)
Maintainer: Timothy C Bates <timothy.c.bates@gmail.com>

Diff between umx versions 2.8.5 dated 2018-10-06 and 2.9.0 dated 2018-12-19

 umx-2.8.5/umx/R/build_run_modify.r                       |only
 umx-2.8.5/umx/R/deprecated.r                             |only
 umx-2.8.5/umx/R/fit_and_reporting.r                      |only
 umx-2.8.5/umx/R/misc_and_utility.r                       |only
 umx-2.8.5/umx/R/tmx.r                                    |only
 umx-2.8.5/umx/R/umx_build_high_level_models.r            |only
 umx-2.8.5/umx/R/umx_fit_umxFitIndices.r                  |only
 umx-2.8.5/umx/R/xmu.r                                    |only
 umx-2.8.5/umx/R/xmu_make_top.R                           |only
 umx-2.8.5/umx/man/figures/ACE.png                        |only
 umx-2.8.5/umx/man/figures/ACE_full_univariate.pdf        |only
 umx-2.8.5/umx/man/figures/ACE_full_univariate.png        |only
 umx-2.8.5/umx/man/figures/umxLatent.graffle              |only
 umx-2.8.5/umx/man/figures/umx_help_figures               |only
 umx-2.8.5/umx/man/xmuMakeThresholdsMatrices.Rd           |only
 umx-2.8.5/umx/man/xmu_make_top.Rd                        |only
 umx-2.9.0/umx/DESCRIPTION                                |   16 
 umx-2.9.0/umx/MD5                                        |  519 +++++++--------
 umx-2.9.0/umx/NAMESPACE                                  |    8 
 umx-2.9.0/umx/NEWS.md                                    |   38 +
 umx-2.9.0/umx/R/build_run_modify.R                       |only
 umx-2.9.0/umx/R/datasets.R                               |    7 
 umx-2.9.0/umx/R/deprecated.R                             |only
 umx-2.9.0/umx/R/fit_and_reporting.R                      |only
 umx-2.9.0/umx/R/misc_and_utility.R                       |only
 umx-2.9.0/umx/R/tmx.R                                    |only
 umx-2.9.0/umx/R/umxACEnew.R                              |only
 umx-2.9.0/umx/R/umx_build_high_level_models.R            |only
 umx-2.9.0/umx/R/umx_build_polychoricMatrix3.R            |  208 ++----
 umx-2.9.0/umx/R/umx_build_umxACEcov_fixed.R              |   59 -
 umx-2.9.0/umx/R/umx_build_umxACEv.R                      |  513 +++-----------
 umx-2.9.0/umx/R/umx_build_umxGxEbiv.R                    |   22 
 umx-2.9.0/umx/R/umx_build_umxSexLim.R                    |   64 -
 umx-2.9.0/umx/R/umx_build_umxSimplex.R                   |  179 ++---
 umx-2.9.0/umx/R/umx_fit_umxFitIndices.R                  |only
 umx-2.9.0/umx/R/umx_fit_umxPlotCPnew.R                   |   89 +-
 umx-2.9.0/umx/R/xmu.R                                    |only
 umx-2.9.0/umx/R/xmu_make_top_twin_models.R               |only
 umx-2.9.0/umx/R/xmu_mean_var_starts.R                    |only
 umx-2.9.0/umx/README.md                                  |    6 
 umx-2.9.0/umx/inst/WORDLIST                              |   87 ++
 umx-2.9.0/umx/man/RMSEA.MxModel.Rd                       |    2 
 umx-2.9.0/umx/man/RMSEA.Rd                               |    2 
 umx-2.9.0/umx/man/RMSEA.summary.mxmodel.Rd               |    2 
 umx-2.9.0/umx/man/dl_from_dropbox.Rd                     |    2 
 umx-2.9.0/umx/man/extractAIC.MxModel.Rd                  |    2 
 umx-2.9.0/umx/man/figures/ACEcovOnMeans.pdf              |only
 umx-2.9.0/umx/man/figures/ACEmatrix.pdf                  |only
 umx-2.9.0/umx/man/figures/ACEmatrix.png                  |only
 umx-2.9.0/umx/man/figures/ACEunivariate.pdf              |only
 umx-2.9.0/umx/man/figures/ACEunivariate.png              |only
 umx-2.9.0/umx/man/figures/GxE.pdf                        |only
 umx-2.9.0/umx/man/figures/GxEbiv.pdf                     |only
 umx-2.9.0/umx/man/figures/formative.pdf                  |only
 umx-2.9.0/umx/man/figures/measurement_invariance.graffle |only
 umx-2.9.0/umx/man/figures/reflective.pdf                 |only
 umx-2.9.0/umx/man/figures/simplex.pdf                    |only
 umx-2.9.0/umx/man/figures/simplex.png                    |binary
 umx-2.9.0/umx/man/figures/sketch.pdf                     |only
 umx-2.9.0/umx/man/figures/sketch.png                     |only
 umx-2.9.0/umx/man/figures/umxEFA.pdf                     |only
 umx-2.9.0/umx/man/figures/umx_help_figures.graffle       |binary
 umx-2.9.0/umx/man/install.OpenMx.Rd                      |    5 
 umx-2.9.0/umx/man/iqdat.Rd                               |    5 
 umx-2.9.0/umx/man/loadings.MxModel.Rd                    |    2 
 umx-2.9.0/umx/man/loadings.Rd                            |    2 
 umx-2.9.0/umx/man/plot.MxModel.Rd                        |   23 
 umx-2.9.0/umx/man/qm.Rd                                  |    5 
 umx-2.9.0/umx/man/reliability.Rd                         |    2 
 umx-2.9.0/umx/man/residuals.MxModel.Rd                   |    2 
 umx-2.9.0/umx/man/tmx_genotypic_effect.Rd                |    2 
 umx-2.9.0/umx/man/tmx_is.identified.Rd                   |    2 
 umx-2.9.0/umx/man/umx-deprecated.Rd                      |    6 
 umx-2.9.0/umx/man/umx.Rd                                 |   38 -
 umx-2.9.0/umx/man/umxACE.Rd                              |  122 ++-
 umx-2.9.0/umx/man/umxACE_cov_fixed.Rd                    |   42 -
 umx-2.9.0/umx/man/umxACEcov.Rd                           |   50 -
 umx-2.9.0/umx/man/umxACEnew.Rd                           |only
 umx-2.9.0/umx/man/umxACEv.Rd                             |  129 +--
 umx-2.9.0/umx/man/umxAPA.Rd                              |   10 
 umx-2.9.0/umx/man/umxAdd1.Rd                             |    2 
 umx-2.9.0/umx/man/umxAlgebra.Rd                          |   13 
 umx-2.9.0/umx/man/umxBrownie.Rd                          |    5 
 umx-2.9.0/umx/man/umxCI.Rd                               |    2 
 umx-2.9.0/umx/man/umxCI_boot.Rd                          |    2 
 umx-2.9.0/umx/man/umxCP.Rd                               |   64 -
 umx-2.9.0/umx/man/umxCPold.Rd                            |   27 
 umx-2.9.0/umx/man/umxCompare.Rd                          |    2 
 umx-2.9.0/umx/man/umxConfint.Rd                          |   16 
 umx-2.9.0/umx/man/umxCov2cor.Rd                          |    2 
 umx-2.9.0/umx/man/umxCovData.Rd                          |    3 
 umx-2.9.0/umx/man/umxDiagnose.Rd                         |    4 
 umx-2.9.0/umx/man/umxDrop1.Rd                            |    2 
 umx-2.9.0/umx/man/umxEFA.Rd                              |    5 
 umx-2.9.0/umx/man/umxEquate.Rd                           |   10 
 umx-2.9.0/umx/man/umxEval.Rd                             |    4 
 umx-2.9.0/umx/man/umxExpCov.Rd                           |    2 
 umx-2.9.0/umx/man/umxExpMeans.Rd                         |    2 
 umx-2.9.0/umx/man/umxFactor.Rd                           |    5 
 umx-2.9.0/umx/man/umxFactorScores.Rd                     |    2 
 umx-2.9.0/umx/man/umxFitIndices.Rd                       |    2 
 umx-2.9.0/umx/man/umxFixAll.Rd                           |    2 
 umx-2.9.0/umx/man/umxGetParameters.Rd                    |    2 
 umx-2.9.0/umx/man/umxGxE.Rd                              |   52 -
 umx-2.9.0/umx/man/umxGxE_window.Rd                       |   35 -
 umx-2.9.0/umx/man/umxGxEbiv.Rd                           |   20 
 umx-2.9.0/umx/man/umxHetCor.Rd                           |    3 
 umx-2.9.0/umx/man/umxIP.Rd                               |   30 
 umx-2.9.0/umx/man/umxIPnew.Rd                            |   57 +
 umx-2.9.0/umx/man/umxJiggle.Rd                           |    2 
 umx-2.9.0/umx/man/umxLabel.Rd                            |    2 
 umx-2.9.0/umx/man/umxLatent.Rd                           |   10 
 umx-2.9.0/umx/man/umxMI.Rd                               |    2 
 umx-2.9.0/umx/man/umxMatrix.Rd                           |   13 
 umx-2.9.0/umx/man/umxModel.Rd                            |   10 
 umx-2.9.0/umx/man/umxModify.Rd                           |   16 
 umx-2.9.0/umx/man/umxPadAndPruneForDefVars.Rd            |    3 
 umx-2.9.0/umx/man/umxPath.Rd                             |   11 
 umx-2.9.0/umx/man/umxPlotACE.Rd                          |    6 
 umx-2.9.0/umx/man/umxPlotACEcov.Rd                       |    6 
 umx-2.9.0/umx/man/umxPlotACEv.Rd                         |    4 
 umx-2.9.0/umx/man/umxPlotCP.Rd                           |    6 
 umx-2.9.0/umx/man/umxPlotCPnew.Rd                        |    7 
 umx-2.9.0/umx/man/umxPlotGxE.Rd                          |    2 
 umx-2.9.0/umx/man/umxPlotIP.Rd                           |    6 
 umx-2.9.0/umx/man/umxPlotSimplex.Rd                      |   17 
 umx-2.9.0/umx/man/umxRAM.Rd                              |   88 +-
 umx-2.9.0/umx/man/umxRAM2Ordinal.Rd                      |   37 -
 umx-2.9.0/umx/man/umxReduce.Rd                           |    4 
 umx-2.9.0/umx/man/umxReduceACE.Rd                        |    2 
 umx-2.9.0/umx/man/umxReduceGxE.Rd                        |    2 
 umx-2.9.0/umx/man/umxRun.Rd                              |   11 
 umx-2.9.0/umx/man/umxSetParameters.Rd                    |    2 
 umx-2.9.0/umx/man/umxSexLim.Rd                           |   28 
 umx-2.9.0/umx/man/umxSimplex.Rd                          |   57 +
 umx-2.9.0/umx/man/umxSummary.MxModel.Rd                  |    2 
 umx-2.9.0/umx/man/umxSummary.Rd                          |   14 
 umx-2.9.0/umx/man/umxSummaryACE.Rd                       |   26 
 umx-2.9.0/umx/man/umxSummaryACEcov.Rd                    |   16 
 umx-2.9.0/umx/man/umxSummaryACEv.Rd                      |   32 
 umx-2.9.0/umx/man/umxSummaryCP.Rd                        |   16 
 umx-2.9.0/umx/man/umxSummaryGxE.Rd                       |   16 
 umx-2.9.0/umx/man/umxSummaryGxEbiv.Rd                    |   16 
 umx-2.9.0/umx/man/umxSummaryIP.Rd                        |   16 
 umx-2.9.0/umx/man/umxSummarySexLim.Rd                    |   24 
 umx-2.9.0/umx/man/umxSummarySimplex.Rd                   |   39 -
 umx-2.9.0/umx/man/umxSuperModel.Rd                       |   21 
 umx-2.9.0/umx/man/umxThresholdMatrix.Rd                  |   48 -
 umx-2.9.0/umx/man/umxTwoStage.Rd                         |    2 
 umx-2.9.0/umx/man/umxUnexplainedCausalNexus.Rd           |    2 
 umx-2.9.0/umx/man/umxValues.Rd                           |    2 
 umx-2.9.0/umx/man/umxVersion.Rd                          |    5 
 umx-2.9.0/umx/man/umxWeightedAIC.Rd                      |    4 
 umx-2.9.0/umx/man/umx_APA_model_CI.Rd                    |    2 
 umx-2.9.0/umx/man/umx_APA_pval.Rd                        |    2 
 umx-2.9.0/umx/man/umx_add_variances.Rd                   |    2 
 umx-2.9.0/umx/man/umx_aggregate.Rd                       |    4 
 umx-2.9.0/umx/man/umx_apply.Rd                           |    2 
 umx-2.9.0/umx/man/umx_array_shift.Rd                     |    5 
 umx-2.9.0/umx/man/umx_as_numeric.Rd                      |    7 
 umx-2.9.0/umx/man/umx_cell_is_on.Rd                      |    5 
 umx-2.9.0/umx/man/umx_check.Rd                           |    2 
 umx-2.9.0/umx/man/umx_check_OS.Rd                        |    2 
 umx-2.9.0/umx/man/umx_check_model.Rd                     |    4 
 umx-2.9.0/umx/man/umx_check_names.Rd                     |    2 
 umx-2.9.0/umx/man/umx_check_parallel.Rd                  |   33 
 umx-2.9.0/umx/man/umx_cont_2_quantiles.Rd                |    5 
 umx-2.9.0/umx/man/umx_cor.Rd                             |    2 
 umx-2.9.0/umx/man/umx_cov2raw.Rd                         |    3 
 umx-2.9.0/umx/man/umx_default_option.Rd                  |    2 
 umx-2.9.0/umx/man/umx_drop_ok.Rd                         |    2 
 umx-2.9.0/umx/man/umx_explode.Rd                         |    2 
 umx-2.9.0/umx/man/umx_explode_twin_names.Rd              |    2 
 umx-2.9.0/umx/man/umx_find_object.Rd                     |    5 
 umx-2.9.0/umx/man/umx_fix_first_loadings.Rd              |    2 
 umx-2.9.0/umx/man/umx_fix_latents.Rd                     |    2 
 umx-2.9.0/umx/man/umx_fun_mean_sd.Rd                     |    2 
 umx-2.9.0/umx/man/umx_get_bracket_addresses.Rd           |    2 
 umx-2.9.0/umx/man/umx_get_checkpoint.Rd                  |    2 
 umx-2.9.0/umx/man/umx_get_options.Rd                     |    2 
 umx-2.9.0/umx/man/umx_graphviz_rank.Rd                   |    5 
 umx-2.9.0/umx/man/umx_grep.Rd                            |    2 
 umx-2.9.0/umx/man/umx_has_CIs.Rd                         |    2 
 umx-2.9.0/umx/man/umx_has_been_run.Rd                    |    2 
 umx-2.9.0/umx/man/umx_has_means.Rd                       |    2 
 umx-2.9.0/umx/man/umx_has_square_brackets.Rd             |    2 
 umx-2.9.0/umx/man/umx_is_MxData.Rd                       |    2 
 umx-2.9.0/umx/man/umx_is_MxMatrix.Rd                     |    2 
 umx-2.9.0/umx/man/umx_is_MxModel.Rd                      |    2 
 umx-2.9.0/umx/man/umx_is_RAM.Rd                          |    2 
 umx-2.9.0/umx/man/umx_is_class.Rd                        |    2 
 umx-2.9.0/umx/man/umx_is_cov.Rd                          |    2 
 umx-2.9.0/umx/man/umx_is_endogenous.Rd                   |    2 
 umx-2.9.0/umx/man/umx_is_exogenous.Rd                    |    2 
 umx-2.9.0/umx/man/umx_is_numeric.Rd                      |    2 
 umx-2.9.0/umx/man/umx_is_ordered.Rd                      |    2 
 umx-2.9.0/umx/man/umx_long2wide.Rd                       |    8 
 umx-2.9.0/umx/man/umx_lower2full.Rd                      |    6 
 umx-2.9.0/umx/man/umx_make.Rd                            |   19 
 umx-2.9.0/umx/man/umx_make_MR_data.Rd                    |    3 
 umx-2.9.0/umx/man/umx_make_TwinData.Rd                   |   18 
 umx-2.9.0/umx/man/umx_make_bin_cont_pair_data.Rd         |    3 
 umx-2.9.0/umx/man/umx_make_fake_data.Rd                  |    3 
 umx-2.9.0/umx/man/umx_make_sql_from_excel.Rd             |    2 
 umx-2.9.0/umx/man/umx_mat2dot.Rd                         |    6 
 umx-2.9.0/umx/man/umx_means.Rd                           |    2 
 umx-2.9.0/umx/man/umx_merge_CIs.Rd                       |    2 
 umx-2.9.0/umx/man/umx_move_file.Rd                       |    2 
 umx-2.9.0/umx/man/umx_msg.Rd                             |   11 
 umx-2.9.0/umx/man/umx_names.Rd                           |    6 
 umx-2.9.0/umx/man/umx_object_as_str.Rd                   |    2 
 umx-2.9.0/umx/man/umx_open.Rd                            |    2 
 umx-2.9.0/umx/man/umx_open_CRAN_page.Rd                  |    4 
 umx-2.9.0/umx/man/umx_pad.Rd                             |    5 
 umx-2.9.0/umx/man/umx_parameters.Rd                      |    2 
 umx-2.9.0/umx/man/umx_paste_names.Rd                     |    8 
 umx-2.9.0/umx/man/umx_pb_note.Rd                         |    4 
 umx-2.9.0/umx/man/umx_polychoric.Rd                      |    7 
 umx-2.9.0/umx/man/umx_polypairwise.Rd                    |    9 
 umx-2.9.0/umx/man/umx_polytriowise.Rd                    |    9 
 umx-2.9.0/umx/man/umx_print.Rd                           |    4 
 umx-2.9.0/umx/man/umx_r_test.Rd                          |    2 
 umx-2.9.0/umx/man/umx_read_lower.Rd                      |    3 
 umx-2.9.0/umx/man/umx_rename.Rd                          |    7 
 umx-2.9.0/umx/man/umx_rename_file.Rd                     |    2 
 umx-2.9.0/umx/man/umx_reorder.Rd                         |    3 
 umx-2.9.0/umx/man/umx_residualize.Rd                     |    2 
 umx-2.9.0/umx/man/umx_rot.Rd                             |    2 
 umx-2.9.0/umx/man/umx_round.Rd                           |    2 
 umx-2.9.0/umx/man/umx_scale.Rd                           |   28 
 umx-2.9.0/umx/man/umx_scale_wide_twin_data.Rd            |    2 
 umx-2.9.0/umx/man/umx_score_scale.Rd                     |only
 umx-2.9.0/umx/man/umx_set_auto_plot.Rd                   |    2 
 umx-2.9.0/umx/man/umx_set_auto_run.Rd                    |    2 
 umx-2.9.0/umx/man/umx_set_checkpoint.Rd                  |    2 
 umx-2.9.0/umx/man/umx_set_condensed_slots.Rd             |    2 
 umx-2.9.0/umx/man/umx_set_cores.Rd                       |    2 
 umx-2.9.0/umx/man/umx_set_optimization_options.Rd        |    2 
 umx-2.9.0/umx/man/umx_set_optimizer.Rd                   |    2 
 umx-2.9.0/umx/man/umx_set_plot_file_suffix.Rd            |    2 
 umx-2.9.0/umx/man/umx_set_plot_format.Rd                 |    2 
 umx-2.9.0/umx/man/umx_set_table_format.Rd                |    2 
 umx-2.9.0/umx/man/umx_show.Rd                            |    2 
 umx-2.9.0/umx/man/umx_show_fit_or_comparison.Rd          |    2 
 umx-2.9.0/umx/man/umx_stack.Rd                           |    3 
 umx-2.9.0/umx/man/umx_standardize.Rd                     |    2 
 umx-2.9.0/umx/man/umx_standardize_ACE.Rd                 |    6 
 umx-2.9.0/umx/man/umx_standardize_ACEcov.Rd              |    2 
 umx-2.9.0/umx/man/umx_standardize_ACEv.Rd                |    8 
 umx-2.9.0/umx/man/umx_standardize_CP.Rd                  |    2 
 umx-2.9.0/umx/man/umx_standardize_IP.Rd                  |    2 
 umx-2.9.0/umx/man/umx_standardize_RAM.Rd                 |    4 
 umx-2.9.0/umx/man/umx_standardize_Simplex.Rd             |    6 
 umx-2.9.0/umx/man/umx_string_to_algebra.Rd               |    2 
 umx-2.9.0/umx/man/umx_swap_a_block.Rd                    |   11 
 umx-2.9.0/umx/man/umx_time.Rd                            |    2 
 umx-2.9.0/umx/man/umx_trim.Rd                            |    2 
 umx-2.9.0/umx/man/umx_var.Rd                             |    2 
 umx-2.9.0/umx/man/umx_wide2long.Rd                       |    2 
 umx-2.9.0/umx/man/umx_write_to_clipboard.Rd              |    2 
 umx-2.9.0/umx/man/xmuHasSquareBrackets.Rd                |   10 
 umx-2.9.0/umx/man/xmuLabel_MATRIX_Model.Rd               |   10 
 umx-2.9.0/umx/man/xmuLabel_Matrix.Rd                     |   10 
 umx-2.9.0/umx/man/xmuLabel_RAM_Model.Rd                  |   10 
 umx-2.9.0/umx/man/xmuMI.Rd                               |   10 
 umx-2.9.0/umx/man/xmuMakeDeviationThresholdsMatrices.Rd  |   10 
 umx-2.9.0/umx/man/xmuMakeOneHeadedPathsFromPathList.Rd   |   10 
 umx-2.9.0/umx/man/xmuMakeTwoHeadedPathsFromPathList.Rd   |   10 
 umx-2.9.0/umx/man/xmuMaxLevels.Rd                        |   10 
 umx-2.9.0/umx/man/xmuMinLevels.Rd                        |   10 
 umx-2.9.0/umx/man/xmuPropagateLabels.Rd                  |   10 
 umx-2.9.0/umx/man/xmu_assemble_twin_supermodel.Rd        |only
 umx-2.9.0/umx/man/xmu_check_levels_identical.Rd          |   10 
 umx-2.9.0/umx/man/xmu_dot_make_paths.Rd                  |   10 
 umx-2.9.0/umx/man/xmu_dot_make_residuals.Rd              |   10 
 umx-2.9.0/umx/man/xmu_dot_maker.Rd                       |   12 
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Package Rlibeemd updated to version 1.4.1 with previous version 1.4.0 dated 2017-10-24

Title: Ensemble Empirical Mode Decomposition (EEMD) and Its Complete Variant (CEEMDAN)
Description: An R interface for libeemd (Luukko, Helske, Räsänen, 2016) <doi:10.1007/s00180-015-0603-9>, a C library of highly efficient parallelizable functions for performing the ensemble empirical mode decomposition (EEMD), its complete variant (CEEMDAN), the regular empirical mode decomposition (EMD), and bivariate EMD (BEMD). Due to the possible portability issues CRAN version no longer supports OpenMP, you can install OpenMP-supported version from GitHub: <https://github.com/helske/Rlibeemd/>.
Author: Jouni Helske [aut, cre] (R interface, <https://orcid.org/0000-0001-7130-793X>), Perttu Luukko [aut] (Original libeemd C library, <https://orcid.org/0000-0003-3786-9685>)
Maintainer: Jouni Helske <jouni.helske@iki.fi>

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Package osmplotr updated to version 0.3.2 with previous version 0.3.0 dated 2017-06-30

Title: Bespoke Images of 'OpenStreetMap' Data
Description: Bespoke images of 'OpenStreetMap' ('OSM') data and data visualisation using 'OSM' objects.
Author: Mark Padgham [aut, cre], Richard Beare [aut], Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>

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Package extremefit updated to version 1.0.0 with previous version 0.2.5 dated 2018-12-11

Title: Estimation of Extreme Conditional Quantiles and Probabilities
Description: Extreme value theory, nonparametric kernel estimation, tail conditional probabilities, extreme conditional quantile, adaptive estimation, quantile regression, survival probabilities.
Author: Gilles Durrieu, Ion Grama, Kevin Jaunatre, Quang-Khoai Pham, Jean-Marie Tricot
Maintainer: Kevin Jaunatre <kevin.jaunatre@univ-ubs.fr>

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Package rbacon updated to version 2.3.5 with previous version 2.3.4 dated 2018-04-15

Title: Age-Depth Modelling using Bayesian Statistics
Description: Bacon is an approach to age-depth modelling that uses Bayesian statistics to reconstruct accumulation histories for deposits, through combining radiocarbon and other dates with prior information. See Blaauw & Christen (2011) <doi:10.1214/11-BA618>.
Author: Maarten Blaauw [aut, cre], J. Andres Christen [aut], Judith Esquivel Vazquez [ctb], Ted Belding [cph], James Theiler [cph], Brian Gough [cph], Charles Karney [cph]
Maintainer: Maarten Blaauw <maarten.blaauw@qub.ac.uk>

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Package GSODR updated to version 1.3.1 with previous version 1.3.0 dated 2018-11-19

Title: Global Surface Summary of the Day ('GSOD') Weather Data Client
Description: Provides automated downloading, parsing, cleaning, unit conversion and formatting of Global Surface Summary of the Day ('GSOD') weather data from the from the USA National Centers for Environmental Information ('NCEI') for use in R. Units are converted from from United States Customary System ('USCS') units to International System of Units ('SI'). Stations may be individually checked for number of missing days defined by the user, where stations with too many missing observations are omitted. Only stations with valid reported latitude and longitude values are permitted in the final data. Additional useful elements, saturation vapour pressure ('es'), actual vapour pressure ('ea') and relative humidity are calculated from the original data and included in the final data set. The resulting data include station identification information, state, country, latitude, longitude, elevation, weather observations and associated flags. Additional data are included with this R package: a list of elevation values for stations between -60 and 60 degrees latitude derived from the Shuttle Radar Topography Measuring Mission ('SRTM'). For information on the 'GSOD' data from 'NCEI', please see the 'GSOD' 'readme.txt' file available from, <http://www1.ncdc.noaa.gov/pub/data/gsod/readme.txt>.
Author: Adam Sparks [aut, cre] (<https://orcid.org/0000-0002-0061-8359>), Tomislav Hengl [aut] (<https://orcid.org/0000-0002-9921-5129>), Andrew Nelson [aut] (<https://orcid.org/0000-0002-7249-3778>), Hugh Parsonage [cph, ctb] (<https://orcid.org/0000-0003-4055-0835>), Bob Rudis [cph, ctb] (<https://orcid.org/0000-0001-5670-2640>), Gwenael Giboire [ctb] (Several bug reports in early versions and testing feedback), Łukasz Pawlik [ctb] (Reported bug in windspeed conversion calculation), Ross Darnell [ctb] (Reported bug in 'Windows OS' versions causing 'GSOD' data untarring to fail)
Maintainer: Adam Sparks <adamhsparks@gmail.com>

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Package datastructures updated to version 0.2.8 with previous version 0.2.7 dated 2018-08-16

Title: Implementation of Core Data Structures
Description: Implementation of advanced data structures such as hashmaps, heaps, or queues. Advanced data structures are essential in many computer science and statistics problems, for example graph algorithms or string analysis. The package uses 'Boost' and 'STL' data types and extends these to R with 'Rcpp' modules.
Author: Simon Dirmeier [aut, cre]
Maintainer: Simon Dirmeier <simon.dirmeier@web.de>

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Package bgsmtr updated to version 0.3 with previous version 0.2 dated 2018-08-26

Title: Bayesian Group Sparse Multi-Task Regression
Description: Fits a Bayesian group-sparse multi-task regression model using Gibbs sampling. The hierarchical prior encourages shrinkage of the estimated regression coefficients at both the gene and SNP level. The model has been extended to a spatial model that allows for two type correlation in neuroimaging genetics data and been applied successfully to imaging phenotypes of dimension up to 100; it can be used more generally for multivariate (non-imaging) phenotypes.
Author: Yin Song, Shufei Ge, Liangliang Wang, Farouk S. Nathoo, Keelin Greenlaw, Mary Lesperance
Maintainer: Yin Song <yinsong@uvic.ca>

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Package visualFields updated to version 0.6 with previous version 0.5.5 dated 2018-11-12

Title: Statistical Methods for Visual Fields
Description: A collection of tools for analyzing the field of vision. It provides a framework for development and use of innovative methods for visualization, statistical analysis, and clinical interpretation of visual-field loss and its change over time. It is intended to be a tool for collaborative research.
Author: Ivan Marin-Franch <imarinfr@optocom.es>
Maintainer: Ivan Marin-Franch <imarinfr@optocom.es>

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Package RKEELjars updated to version 1.0.19 with previous version 1.0.18 dated 2018-06-27

Title: Java Executable .jar Files for 'RKEEL'
Description: 'KEEL' is a popular Java software for a large number of different knowledge data discovery tasks. Furthermore, 'RKEEL' is a package with a R code layer between R and 'KEEL', for using 'KEEL' in R code. This package downloads and install the .jar files necessary for 'RKEEL' algorithms execution. For more information about 'KEEL', see <http://www.keel.es/>.
Author: Jose M. Moyano [aut, cre], Luciano Sanchez Ramos [aut]
Maintainer: Jose M. Moyano <jmoyano@uco.es>

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Package ggtern updated to version 3.1.0 with previous version 3.0.0.1 dated 2018-11-06

Title: An Extension to 'ggplot2', for the Creation of Ternary Diagrams
Description: Extends the functionality of 'ggplot2', providing the capability to plot ternary diagrams for (subset of) the 'ggplot2' geometries. Additionally, 'ggtern' has implemented several NEW geometries which are unavailable to the standard 'ggplot2' release. For further examples and documentation, please proceed to the 'ggtern' website.
Author: Nicholas Hamilton [aut, cre]
Maintainer: Nicholas Hamilton <nick@ggtern.com>

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More information about ggtern at CRAN
Permanent link

Package rcrtan updated to version 0.1.1 with previous version 0.1.0 dated 2018-08-17

Title: Criterion-Referenced Test Analysis
Description: Contains methods for criterion-referenced test analyses as described in Brown & Hudson (2002). This includes cut-score item discrimination analyses and measures of dependability.
Author: Geoffrey T. LaFlair
Maintainer: Geoffrey T. LaFlair <gtlaflair@gmail.com>

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More information about rcrtan at CRAN
Permanent link

Package osmdata updated to version 0.0.9 with previous version 0.0.8 dated 2018-10-22

Title: Import 'OpenStreetMap' Data as Simple Features or Spatial Objects
Description: Download and import of 'OpenStreetMap' ('OSM') data as 'sf' or 'sp' objects. 'OSM' data are extracted from the 'Overpass' web server and processed with very fast 'C++' routines for return to 'R'.
Author: Mark Padgham [aut, cre], Bob Rudis [aut], Robin Lovelace [aut], Maëlle Salmon [aut], Andrew Smith [ctb], James Smith [ctb], Marcin Kalicinski [ctb, cph] (Author of included RapidXML code), Finkelstein Noam [ctb, cph] (Author of included stub.R code), Bartnik Lukasz [ctb, cph] (Author of included stub.R code)
Maintainer: Mark Padgham <mark.padgham@email.com>

Diff between osmdata versions 0.0.8 dated 2018-10-22 and 0.0.9 dated 2018-12-19

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More information about osmdata at CRAN
Permanent link

Package colourvalues updated to version 0.2.1 with previous version 0.2.0 dated 2018-11-07

Title: Assigns Colours to Values
Description: Maps one of the viridis colour palettes, or a user-specified palette to values. Viridis colour maps are created by Stéfan van der Walt and Nathaniel Smith. They were set as the default palette for the 'Python' 'Matplotlib' library, introduced at SciPy 2015 conference <http://scipy2015.scipy.org/ehome/index.php?eventid=115969&>. Other palettes available in this library have been derived from 'RColorBrewer' <https://CRAN.R-project.org/package=RColorBrewer> and 'colorspace' <https://CRAN.R-project.org/package=colorspace> packages.
Author: David Cooley [aut, cre]
Maintainer: David Cooley <dcooley@symbolix.com.au>

Diff between colourvalues versions 0.2.0 dated 2018-11-07 and 0.2.1 dated 2018-12-19

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 colourvalues-0.2.1/colourvalues/DESCRIPTION                                               |   15 
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Permanent link

Package GenEst updated to version 1.2.1 with previous version 1.2.0 dated 2018-12-06

Title: Generalized Mortality Estimator
Description: Command-line and 'shiny' GUI implementation of the GenEst models for estimating bird and bat mortality at wind and solar power facilities, following Dalthorp, et al. (2018) <doi:10.3133/tm7A2>.
Author: Daniel Dalthorp [aut, cre], Juniper Simonis [aut], Lisa Madsen [aut], Manuela Huso [aut], Paul Rabie [aut], Jeffrey Mintz [aut], Robert Wolpert [aut], Jared Studyvin [aut], Franzi Korner-Nievergelt [aut]
Maintainer: Daniel Dalthorp <ddalthorp@usgs.gov>

Diff between GenEst versions 1.2.0 dated 2018-12-06 and 1.2.1 dated 2018-12-19

 DESCRIPTION                                |   10 
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Tue, 18 Dec 2018

Package r2d3 updated to version 0.2.3 with previous version 0.2.2 dated 2018-05-30

Title: Interface to 'D3' Visualizations
Description: Suite of tools for using 'D3', a library for producing dynamic, interactive data visualizations. Supports translating objects into 'D3' friendly data structures, rendering 'D3' scripts, publishing 'D3' visualizations, incorporating 'D3' in R Markdown, creating interactive 'D3' applications with Shiny, and distributing 'D3' based 'htmlwidgets' in R packages.
Author: Javier Luraschi [aut, cre], JJ Allaire [aut], Mike Bostock [ctb, cph] (d3.js library, http://d3js.org), RStudio [cph]
Maintainer: Javier Luraschi <javier@rstudio.com>

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Package dbarts updated to version 0.9-8 with previous version 0.9-7 dated 2018-12-18

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 0.9-7 dated 2018-12-18 and 0.9-8 dated 2018-12-18

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Package ritis updated to version 0.7.6 with previous version 0.7.2 dated 2018-05-20

Title: Integrated Taxonomic Information System Client
Description: An interface to the Integrated Taxonomic Information System ('ITIS') (<https://www.itis.gov>). Includes functions to work with the 'ITIS' REST API methods (<https://www.itis.gov/ws_description.html>), as well as the 'Solr' web service (<https://www.itis.gov/solr_documentation.html>).
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package drtmle updated to version 1.0.4 with previous version 1.0.3 dated 2018-07-02

Title: Doubly-Robust Nonparametric Estimation and Inference
Description: Targeted minimum loss-based estimators of counterfactual means and causal effects that are doubly-robust with respect both to consistency and asymptotic normality (Benkeser et al (2017), <doi:10.1093/biomet/asx053>; MJ van der Laan (2014), <doi:10.1515/ijb-2012-0038>).
Author: David Benkeser [aut, cre, cph] (<https://orcid.org/0000-0002-1019-8343>), Nima Hejazi [ctb] (<https://orcid.org/0000-0002-7127-2789>)
Maintainer: David Benkeser <benkeser@emory.edu>

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Package LLSR updated to version 0.0.2.5 with previous version 0.0.2.4 dated 2018-12-05

Title: Data Analysis of Liquid-Liquid Systems
Description: Analyses experimental data from liquid-liquid phase diagrams and provide a simple way to obtain its parameters, producing a simplified report. Designed initially to analyse Aqueous Two-Phases Systems, the package will include (every other update) new functions in order to comprise useful tools in liquid-liquid analysis.
Author: Diego F Coelho <diegofcoelho@gmail.com> [aut, cre], Pedro V O Menezes <pedrod841@hotmail.com> [dtc], Carla Corina <carlacorina@hotmail.com.br> [dtc], Jon G Huddleston <Jonathan.Huddleston@brunel.ac.uk> [rev]
Maintainer: Diego F Coelho <diegofcoelho@gmail.com>

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Package chillR updated to version 0.70.12 with previous version 0.70.6 dated 2018-06-29

Title: Statistical Methods for Phenology Analysis in Temperate Fruit Trees
Description: The phenology of plants (i.e. the timing of their annual life phases) depends on climatic cues. For temperate trees and many other plants, spring phases, such as leaf emergence and flowering, have been found to result from the effects of both cool (chilling) conditions and heat. Fruit tree scientists (pomologists) have developed some metrics to quantify chilling and heat (e.g. see Luedeling (2012) <doi.org/10.1016/j.scienta.2012.07.011>). 'chillR' contains functions for processing temperature records into chilling (Chilling Hours, Utah Chill Units and Chill Portions) and heat units (Growing Degree Hours). Regarding chilling metrics, Chill Portions are often considered the most promising, but they are difficult to calculate. This package makes it easy. 'chillR' also contains procedures for conducting a PLS analysis relating phenological dates (e.g. bloom dates) to either mean temperatures or mean chill and heat accumulation rates, based on long-term weather and phenology records (Luedeling and Gassner (2012) <doi.org/10.1016/j.agrformet.2011.10.020>). As of version 0.65, it also includes functions for generating weather scenarios with a weather generator, for conducting climate change analyses for temperature-based climatic metrics and for plotting results from such analyses. Since version 0.70, 'chillR' contains a function for interpolating hourly temperature records.
Author: Eike Luedeling
Maintainer: Eike Luedeling <eike@eikeluedeling.com>

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Package httpuv updated to version 1.4.5.1 with previous version 1.4.5 dated 2018-07-19

Title: HTTP and WebSocket Server Library
Description: Provides low-level socket and protocol support for handling HTTP and WebSocket requests directly from within R. It is primarily intended as a building block for other packages, rather than making it particularly easy to create complete web applications using httpuv alone. httpuv is built on top of the libuv and http-parser C libraries, both of which were developed by Joyent, Inc. (See LICENSE file for libuv and http-parser license information.)
Author: Joe Cheng, Hector Corrada Bravo [ctb], Jeroen Ooms [ctb], Winston Chang [ctb]
Maintainer: Joe Cheng <joe@rstudio.com>

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Package citr updated to version 0.3.0 with previous version 0.2.0 dated 2016-09-20

Title: 'RStudio' Add-in to Insert Markdown Citations
Description: Functions and an 'RStudio' add-in that search a 'Bib(La)TeX'-file to create and insert formatted Markdown citations into the current document.
Author: Frederik Aust [aut, cre] (<https://orcid.org/0000-0003-4900-788X>), Yihui Xie [ctb], Robin Lovelace [ctb], Garrick Aden-Buie [ctb]
Maintainer: Frederik Aust <frederik.aust@uni-koeln.de>

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Package TreeBUGS updated to version 1.4.1 with previous version 1.4.0 dated 2018-05-15

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], Nina R. Arnold [aut, dtc], Denis Arnold [aut], Alexander Ly [ctb]
Maintainer: Daniel W. Heck <heck@uni-mannheim.de>

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Package sjPlot updated to version 2.6.2 with previous version 2.6.1 dated 2018-10-14

Title: Data Visualization for Statistics in Social Science
Description: Collection of plotting and table output functions for data visualization. Results of various statistical analyses (that are commonly used in social sciences) can be visualized using this package, including simple and cross tabulated frequencies, histograms, box plots, (generalized) linear models, mixed effects models, principal component analysis and correlation matrices, cluster analyses, scatter plots, stacked scales, effects plots of regression models (including interaction terms) and much more. This package supports labelled data.
Author: Daniel Lüdecke [aut, cre] (<https://orcid.org/0000-0002-8895-3206>), Carsten Schwemmer [ctb]
Maintainer: Daniel Lüdecke <d.luedecke@uke.de>

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Package RFishBC updated to version 0.2.0 with previous version 0.1.1 dated 2018-11-18

Title: Back-Calculation of Fish Length
Description: Helps fisheries scientists collect measurements from calcified structures and back-calculate estimated lengths at previous ages using standard procedures and models. This is intended to replace much of the functionality provided by the now out-dated 'fishBC' software.
Author: Derek Ogle [aut, cre] (<https://orcid.org/0000-0002-0370-9299>)
Maintainer: Derek Ogle <derek@derekogle.com>

Diff between RFishBC versions 0.1.1 dated 2018-11-18 and 0.2.0 dated 2018-12-18

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Package blocksdesign updated to version 3.2 with previous version 3.1 dated 2018-10-18

Title: Nested and Crossed Block Designs for Factorial, Fractional Factorial and Unstructured Treatment Sets
Description: Constructs D-optimal or near D-optimal nested and crossed block designs for unstructured or general factorial treatment designs. The treatment design, if required, is found from a defined model matrix design formula. The block design is found from a defined set of block factors and is conditional on the defined treatment design. The block factors are added in sequence and each added block factor is optimized conditional on all previously added block factors. The block design can have repeated nesting down to any required depth of nesting with either simple nested blocks or a crossed blocks design at each level of nesting. Outputs include a table showing the allocation of treatments to blocks and tables showing the achieved D-efficiency factors for each block and treatment design.
Author: R. N. Edmondson.
Maintainer: Rodney Edmondson <rodney.edmondson@gmail.com>

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Package EpiModel updated to version 1.7.2 with previous version 1.7.0 dated 2018-11-21

Title: Mathematical Modeling of Infectious Disease Dynamics
Description: Tools for simulating mathematical models of infectious disease dynamics. Epidemic model classes include deterministic compartmental models, stochastic individual-contact models, and stochastic network models. Network models use the robust statistical methods of exponential-family random graph models (ERGMs) from the Statnet suite of software packages in R. Standard templates for epidemic modeling include SI, SIR, and SIS disease types. EpiModel features an API for extending these templates to address novel scientific research aims.
Author: Samuel Jenness [cre, aut], Steven M. Goodreau [aut], Martina Morris [aut], Emily Beylerian [ctb], Skye Bender-deMoll [ctb], Kevin Weiss [ctb], Shawnee Anderson [ctb]
Maintainer: Samuel Jenness <samuel.m.jenness@emory.edu>

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Package dbarts updated to version 0.9-7 with previous version 0.9-5 dated 2018-07-07

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>

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Package CornerstoneR updated to version 1.0.1 with previous version 1.0.0 dated 2018-12-16

Title: Collection for 'CornerstoneR' Interface
Description: Collection of scripts for interface between 'Cornerstone' and 'R'. 'Cornerstone' (<https://www.camline.com/>) is a software for engineering analytics which supports an interface to 'R'. The scripts are designed to support an easy usage of this interface.
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>

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Package rmumps updated to version 5.1.2-5 with previous version 5.1.2-4 dated 2018-01-05

Title: Wrapper for MUMPS Library
Description: Some basic features of MUMPS (Multifrontal Massively Parallel sparse direct Solver) are wrapped in a class whose methods can be used for sequentially solving a sparse linear system (symmetric or not) with one or many right hand sides (dense or sparse). There is a possibility to do separately symbolic analysis, LU (or LDL^t) factorization and system solving. Third part ordering libraries are included and can be used: PORD, METIS, SCOTCH. MUMPS method was first described in Amestoy et al. (2001) <doi:10.1137/S0895479899358194> and Amestoy et al. (2006) <doi:10.1016/j.parco.2005.07.004>.
Author: Serguei Sokol [aut, cre], Emmanuel Agullo [ctb], Patrick Amestoy [ctb], Maurice Bremond [ctb], Alfredo Buttari [ctb], Philippe Combes [ctb], Marie Durand [ctb], Aurelia Fevre [ctb], Abdou Guermouche [ctb], Guillaume Joslin [ctb], Jacko Koster [ctb], Jean-Yves L'Excellent [ctb], Stephane Pralet [ctb], Chiara Puglisi [ctb], Francois-Henry Rouet [ctb], Wissam Sid-Lakhdar [ctb], Tzvetomila Slavova [ctb], Bora Ucar [ctb], Clement Weisbecker [ctb], Juergen Schulze [ctb], George Karypis [ctb], Douglas C. Schmidt [ctb], Isamu Hasegawa [ctb], Alexander Chemeris [ctb], Makoto Matsumoto [ctb], Takuji Nishimura [ctb], Francois Pellegrini [ctb], David Goudin [ctb], Pascal Henon [ctb], Pierre Ramet [ctb], Sebastien Fourestier [ctb], Jun-Ho Her [ctb], Cedric Chevalier [ctb], Timothy A. Davis [ctb], Iain S. Duff [ctb], John K. Reid [ctb], Richard Stallman [ctb], Samuel Thibault [ctb]
Maintainer: Serguei Sokol <sokol@insa-toulouse.fr>

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Package finalfit updated to version 0.8.9 with previous version 0.8.8 dated 2018-11-09

Title: Quickly Create Elegant Regression Results Tables and Plots when Modelling
Description: Generate regression results tables and plots in final format for publication. Explore models and export directly to PDF and 'Word' using 'RMarkdown'.
Author: Ewen Harrison [aut, cre], Tom Drake [aut], Riinu Ots [aut]
Maintainer: Ewen Harrison <ewen.harrison@ed.ac.uk>

Diff between finalfit versions 0.8.8 dated 2018-11-09 and 0.8.9 dated 2018-12-18

 DESCRIPTION                                                                        |   10 
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 NAMESPACE                                                                          |   12 
 NEWS.md                                                                            |    9 
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 R/ff_interaction.R                                                                 |   17 
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 R/finalfit.R                                                                       |    3 
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 R/finalfit_package.R                                                               |   10 
 R/fit2df.R                                                                         |    2 
 R/hr_plot.R                                                                        |    4 
 R/missing_glimpse.R                                                                |    5 
 R/or_plot.R                                                                        |  216 +++++-----
 R/summaryfactorlist.R                                                              |    5 
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 man/or_plot.Rd                                                                     |   28 -
 man/surv_plot.Rd                                                                   |    3 
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 tests/testthat/Rplots.pdf                                                          |binary
 tests/testthat/test_internals.R                                                    |   30 +
 tests/testthat/test_plots.R                                                        |   19 
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Package sentometrics updated to version 0.5.6 with previous version 0.5.5 dated 2018-11-15

Title: An Integrated Framework for Textual Sentiment Time Series Aggregation and Prediction
Description: Optimized prediction based on textual sentiment, accounting for the intrinsic challenge that sentiment can be computed and pooled across texts and time in various ways. See Ardia et al. (2018) <doi:10.2139/ssrn.3067734>.
Author: David Ardia [aut], Keven Bluteau [aut], Samuel Borms [aut, cre], Kris Boudt [aut]
Maintainer: Samuel Borms <samuel.borms@unine.ch>

Diff between sentometrics versions 0.5.5 dated 2018-11-15 and 0.5.6 dated 2018-12-18

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 README.md                         |    2 
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Package smotefamily updated to version 1.3 with previous version 1.2 dated 2018-01-30

Title: A Collection of Oversampling Techniques for Class Imbalance Problem Based on SMOTE
Description: A collection of various oversampling techniques developed from SMOTE is provided. SMOTE is a oversampling technique which synthesizes a new minority instance between a pair of one minority instance and one of its K nearest neighbor. (see <https://www.jair.org/media/953/live-953-2037-jair.pdf> for more information) Other techniques adopt this concept with other criteria in order to generate balanced dataset for class imbalance problem.
Author: Wacharasak Siriseriwan [aut, cre]
Maintainer: Wacharasak Siriseriwan <wacharasak.s@gmail.com>

Diff between smotefamily versions 1.2 dated 2018-01-30 and 1.3 dated 2018-12-18

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Package prettyGraphs updated to version 2.1.6 with previous version 2.1.5 dated 2013-12-10

Title: Publication-Quality Graphics
Description: Simple and crisp publication-quality graphics for the ExPosition family of packages. See An ExPosition of the Singular Value Decomposition in R (Beaton et al 2014) <doi:10.1016/j.csda.2013.11.006>.
Author: Derek Beaton
Maintainer: Derek Beaton <exposition.software@gmail.com>

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Package PELVIS updated to version 1.0.5 with previous version 1.0.4 dated 2018-08-05

Title: Probabilistic Sex Estimate using Logistic Regression, Based on VISual Traits of the Human Os Coxae
Description: An R-Shiny application implementing two methods for sexing the human os coxae based on eleven trichotomic traits, following Bruzek (2002) <doi:10.1002/ajpa.10012>.
Author: Frédéric Santos [aut, cre] (<https://orcid.org/0000-0003-1445-3871>)
Maintainer: Frédéric Santos <frederic.santos@u-bordeaux.fr>

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Package dynRB updated to version 0.15 with previous version 0.13 dated 2018-07-13

Title: Dynamic Range Boxes
Description: Improves the concept of multivariate range boxes, which is highly susceptible for outliers and does not consider the distribution of the data. The package uses dynamic range boxes to overcome these problems.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>, Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>, Robert R. Junker <Robert.Junker@sbg.ac.at>, Jonas Kuppler <Jonas.Kuppler@uni-duesseldorf.de>, Arne Bathke <Arne.Bathke@sbg.ac.at>, Judith H. Parkinson <judith.parkinson@sbg.ac.at>, Raoul Kutil <Raoul_Hugo.Kutil@stud.sbg.ac.at>
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>

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Package cubature updated to version 2.0.3 with previous version 2.0.2 dated 2018-12-11

Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector interfaces for cubature and Cuba routines are provided; the vector interfaces are highly recommended as demonstrated in the package vignette.
Author: Balasubramanian Narasimhan [aut, cre], Manuel Koller [ctb], Steven G. Johnson [aut], Thomas Hahn [aut], Annie Bouvier [aut], Kiên Kiêu [aut], Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>

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Package CRF updated to version 0.4-0 with previous version 0.3-16 dated 2018-05-07

Title: Conditional Random Fields
Description: Implements modeling and computational tools for conditional random fields (CRF) model as well as other probabilistic undirected graphical models of discrete data with pairwise and unary potentials.
Author: Ling-Yun Wu [aut, cre]
Maintainer: Ling-Yun Wu <wulingyun@gmail.com>

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Package classInt updated to version 0.3-1 with previous version 0.2-3 dated 2018-04-16

Title: Choose Univariate Class Intervals
Description: Selected commonly used methods for choosing univariate class intervals for mapping or other graphics purposes.
Author: Roger Bivand [aut, cre] (<https://orcid.org/0000-0003-2392-6140>), Hisaji Ono [ctb], Richard Dunlap [ctb], Matthieu Stigler [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>

Diff between classInt versions 0.2-3 dated 2018-04-16 and 0.3-1 dated 2018-12-18

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Package ChaosGame updated to version 0.4 with previous version 0.3 dated 2017-07-20

Title: Chaos Game
Description: The main objective of the package is to enter a word of at least two letters based on which an Iterated Function System with Probabilities is constructed, and a two-dimensional fractal containing the chosen word infinitely often is generated via the Chaos Game. Additionally, the package allows to project the two-dimensional fractal on several three-dimensional surfaces and to transform the fractal into another fractal with uniform marginals.
Author: Manuela Schreyer <manuelalarissa.schreyer@sbg.ac.at>, Wolfgang Trutschnig <Wolfgang.Trutschnig@sbg.ac.at>
Maintainer: Florian Griessenberger <florian.griessenberger@sbg.ac.at>

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Package quantreg updated to version 5.38 with previous version 5.36 dated 2018-05-29

Title: Quantile Regression
Description: Estimation and inference methods for models of conditional quantiles: Linear and nonlinear parametric and non-parametric (total variation penalized) models for conditional quantiles of a univariate response and several methods for handling censored survival data. Portfolio selection methods based on expected shortfall risk are also included.
Author: Roger Koenker [cre, aut], Stephen Portnoy [ctb] (Contributions to Censored QR code), Pin Tian Ng [ctb] (Contributions to Sparse QR code), Achim Zeileis [ctb] (Contributions to dynrq code essentially identical to his dynlm code), Philip Grosjean [ctb] (Contributions to nlrq code), Brian D Ripley [trl, ctb] (Initial (2001) R port from S (to my everlasting shame -- how could I have been so slow to adopt R!) and for numerous other suggestions and useful advice)
Maintainer: Roger Koenker <rkoenker@illinois.edu>

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Package Corbi updated to version 0.4-3 with previous version 0.4-2 dated 2017-05-03

Title: Collection of Rudimentary Bioinformatics Tools
Description: Provides a bundle of basic and fundamental bioinformatics tools, such as network querying and alignment, subnetwork extraction and search, network biomarker identification.
Author: Ling-Yun Wu [aut, cre], Qiang Huang [aut], Duanchen Sun [aut]
Maintainer: Ling-Yun Wu <wulingyun@gmail.com>

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Package breathtestcore updated to version 0.4.6 with previous version 0.4.5 dated 2018-10-17

Title: Core Functions to Read and Fit 13c Time Series from Breath Tests
Description: Reads several formats of 13C data (IRIS/Wagner, BreathID) and CSV. Creates artificial sample data for testing. Fits Maes/Ghoos, Bluck-Coward self-correcting formula using 'nls', 'nlme'. Methods to fit breath test curves with Bayesian Stan methods are refactored to package 'breathteststan'. For a Shiny GUI, see package 'dmenne/breathtestshiny' on github.
Author: Dieter Menne [aut, cre], Menne Biomed Consulting Tuebingen [cph], Benjamin Misselwitz [fnd], Mark Fox [fnd], Andreas Steingoetter [dtc], University Hospital of Zurich, Dep. Gastroenterology [fnd, dtc]
Maintainer: Dieter Menne <dieter.menne@menne-biomed.de>

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Package adegraphics updated to version 1.0-15 with previous version 1.0-12 dated 2018-08-31

Title: An S4 Lattice-Based Package for the Representation of Multivariate Data
Description: Graphical functionalities for the representation of multivariate data. It is a complete re-implementation of the functions available in the 'ade4' package.
Author: Stéphane Dray <stephane.dray@univ-lyon1.fr> and Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>, with contributions from Jean Thioulouse. Based on earlier work by Alice Julien-Laferrière.
Maintainer: Aurélie Siberchicot <aurelie.siberchicot@univ-lyon1.fr>

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Mon, 17 Dec 2018

Package survey updated to version 3.35 with previous version 3.34 dated 2018-10-12

Title: Analysis of Complex Survey Samples
Description: Summary statistics, two-sample tests, rank tests, generalised linear models, cumulative link models, Cox models, loglinear models, and general maximum pseudolikelihood estimation for multistage stratified, cluster-sampled, unequally weighted survey samples. Variances by Taylor series linearisation or replicate weights. Post-stratification, calibration, and raking. Two-phase subsampling designs. Graphics. PPS sampling without replacement. Principal components, factor analysis.
Author: Thomas Lumley
Maintainer: "Thomas Lumley" <t.lumley@auckland.ac.nz>

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Package rfUtilities updated to version 2.1-4 with previous version 2.1-3 dated 2018-02-21

Title: Random Forests Model Selection and Performance Evaluation
Description: Utilities for Random Forest model selection, class balance correction, significance test, cross validation and partial dependency plots.
Author: Jeffrey S. Evans [cre, aut], Melanie A. Murphy [ctb]
Maintainer: Jeffrey S. Evans <jeffrey_evans@tnc.org>

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Package geometa updated to version 0.4-0 with previous version 0.3-0 dated 2018-08-22

Title: Tools for Reading and Writing ISO/OGC Geographic Metadata
Description: Provides facilities to handle reading and writing of geographic metadata defined with OGC/ISO 19115, 11119 and 19110 geographic information metadata standards, and encoded using the ISO 19139 (XML) standard. It includes also a facility to check the validity of ISO 19139 XML encoded metadata.
Author: Emmanuel Blondel [aut, cre] (<https://orcid.org/0000-0002-5870-5762>)
Maintainer: Emmanuel Blondel <emmanuel.blondel1@gmail.com>

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Package spelling updated to version 2.0 with previous version 1.2 dated 2018-07-09

Title: Tools for Spell Checking in R
Description: Spell checking common document formats including latex, markdown, manual pages, and description files. Includes utilities to automate checking of documentation and vignettes as a unit test during 'R CMD check'. Both British and American English are supported out of the box and other languages can be added. In addition, packages may define a 'wordlist' to allow custom terminology without having to abuse punctuation.
Author: Jeroen Ooms [cre, aut], Jim Hester [aut]
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package Eagle updated to version 1.2.0 with previous version 1.1.0 dated 2018-08-22

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>

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Package vtreat updated to version 1.3.3 with previous version 1.3.2 dated 2018-11-05

Title: A Statistically Sound 'data.frame' Processor/Conditioner
Description: A 'data.frame' processor/conditioner that prepares real-world data for predictive modeling in a statistically sound manner. 'vtreat' prepares variables so that data has fewer exceptional cases, making it easier to safely use models in production. Common problems 'vtreat' defends against: 'Inf', 'NA', too many categorical levels, rare categorical levels, and new categorical levels (levels seen during application, but not during training). Reference: "'vtreat': a data.frame Processor for Predictive Modeling", 'Zumel', 'Mount', 2016, DOI:10.5281/zenodo.1173314.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package WVPlots updated to version 1.0.7 with previous version 1.0.6 dated 2018-11-06

Title: Common Plots for Analysis
Description: Select data analysis plots, under a standardized calling interface implemented on top of 'ggplot2' and 'plotly'. Plots of interest include: 'ROC', gain curve, scatter plot with marginal distributions, conditioned scatter plot with marginal densities, box and stem with matching theoretical distribution, and density with matching theoretical distribution.
Author: John Mount [aut, cre], Nina Zumel [aut], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package cgmanalysis updated to version 2.1 with previous version 2.0 dated 2018-08-23

Title: Clean and Analyze Continuous Glucose Monitor Data
Description: This code provides several different functions for cleaning and analyzing continuous glucose monitor data. Currently it works with 'Dexcom' (<https://www.dexcom.com>), 'iPro 2' (<http://professional.medtronicdiabetes.com/ipro2-professional-cgm>), Diasend (<https://diasend.com//us>), Libre (<https://www.freestylelibre.us/>) or Carelink (<https://www.medtronicdiabetes.com/products/carelink-personal-diabetes-software>) data. The cleandata() function takes a directory of CGM data files and prepares them for analysis. cgmvariables() iterates through a directory of cleaned CGM data files and produces a single spreadsheet with data for each file in either rows or columns. The column format of this spreadsheet is compatible with REDCap data upload ("--1" is added to each subject ID automatically for double data entry). cgmreport() also iterates through a directory of cleaned data, and produces PDFs of individual and aggregate AGP plots. Please visit <https://github.com/childhealthbiostatscore/R-Packages/> to download the new-user guide.
Author: Tim Vigers [aut, cre]
Maintainer: Tim Vigers <tim.b.vigers@gmail.com>

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Package rqdatatable updated to version 1.1.2 with previous version 1.1.1 dated 2018-09-20

Title: 'rquery' for 'data.table'
Description: Implements the 'rquery' piped Codd-style query algebra using 'data.table'. This allows for a high-speed in memory implementation of Codd-style data manipulation tools.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package kdevine updated to version 0.4.2 with previous version 0.4.1 dated 2017-05-19

Title: Multivariate Kernel Density Estimation with Vine Copulas
Description: Implements the vine copula based kernel density estimator of Nagler and Czado (2016) <doi:10.1016/j.jmva.2016.07.003>. The estimator does not suffer from the curse of dimensionality and is therefore well suited for high-dimensional applications.
Author: Thomas Nagler [aut, cre]
Maintainer: Thomas Nagler <thomas.nagler@tum.de>

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Package brms updated to version 2.7.0 with previous version 2.6.0 dated 2018-10-23

Title: Bayesian Regression Models using 'Stan'
Description: Fit Bayesian generalized (non-)linear multivariate multilevel models using 'Stan' for full Bayesian inference. A wide range of distributions and link functions are supported, allowing users to fit -- among others -- linear, robust linear, count data, survival, response times, ordinal, zero-inflated, hurdle, and even self-defined mixture models all in a multilevel context. Further modeling options include non-linear and smooth terms, auto-correlation structures, censored data, meta-analytic standard errors, and quite a few more. In addition, all parameters of the response distribution can be predicted in order to perform distributional regression. Prior specifications are flexible and explicitly encourage users to apply prior distributions that actually reflect their beliefs. Model fit can easily be assessed and compared with posterior predictive checks and leave-one-out cross-validation. References: Bürkner (2017) <doi:10.18637/jss.v080.i01>; Carpenter et al. (2017) <doi:10.18637/jss.v076.i01>.
Author: Paul-Christian Bürkner [aut, cre]
Maintainer: Paul-Christian Bürkner <paul.buerkner@gmail.com>

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Package Rcan updated to version 1.3.64 with previous version 1.3.63 dated 2018-12-14

Title: Cancer Registry Data Analysis and Visualisation
Description: Tools for basic and advance cancer statistics and graphics. Calculates age-specific rate, age-standardized rate, estimated annual percentage rate with standards error. Creates graphics across variable and time, such as age-specific trends and period-cohort trends.
Author: Mathieu Laversanne [aut, cre], Cancer Surveillance Unit [cph]
Maintainer: Mathieu Laversanne <laversannem@iarc.fr>

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Package HCmodelSets updated to version 1.0.2 with previous version 1.0.1 dated 2018-12-13

Title: Regression with a Large Number of Potential Explanatory Variables
Description: Software for performing the reduction, exploratory and model selection phases of the procedure proposed by Cox, D.R. and Battey, H.S. (2017) <doi:10.1073/pnas.1703764114> for sparse regression when the number of potential explanatory variables far exceeds the sample size. The software supports linear regression, likelihood-based fitting of generalized linear regression models and the proportional hazards model fitted by partial likelihood.
Author: H. H. Hoeltgebaum
Maintainer: H. H. Hoeltgebaum <hh3015@ic.ac.uk>

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Package stratEst updated to version 0.1.1 with previous version 0.1.0 dated 2018-10-19

Title: Strategy Estimation
Description: Implements variants of the strategy frequency estimation method by Dal Bo & Frechette (2011) <doi:10.1257/aer.101.1.411>, including its adaptation to behavioral memory-one Markov strategies by Breitmoser (2015) <doi:10.1257/aer.20130675>, and the extension in the spirit of latent-class regression by Dvorak & Fehrler (2018) <doi:10.2139/ssrn.2986445>.
Author: Fabian Dvorak
Maintainer: Fabian Dvorak <fabian.dvorak@uni.kn>

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Package Compositional updated to version 3.2 with previous version 3.1 dated 2018-06-04

Title: Compositional Data Analysis
Description: Regression, classification, contour plots, hypothesis testing and fitting of distributions for compositional data are some of the functions included. The standard textbook for such data is John Aitchison's (1986). "The statistical analysis of compositional data". Chapman & Hall.
Author: Michail Tsagris [aut, cre], Giorgos Athineou [aut]
Maintainer: Michail Tsagris <mtsagris@yahoo.gr>

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Package ahpsurvey updated to version 0.3.0 with previous version 0.2.2 dated 2018-09-27

Title: Analytic Hierarchy Process for Survey Data
Description: The Analytic Hierarchy Process is a versatile multi-criteria decision-making tool introduced by Saaty (1987) <doi:10.1016/0270-0255(87)90473-8> that allows decision-makers to weigh attributes and evaluate alternatives presented to them. This package provides a consistent methodology for researchers to reformat data and run analytic hierarchy process in R on data that are formatted using the survey data entry mode. It is optimized for performing the analytic hierarchy process with many decision-makers, and provides tools and options for researchers to aggregate individual preferences and test multiple options. It also allows researchers to quantify, visualize and correct for inconsistency in the decision-maker's comparisons.
Author: Frankie Cho [aut, cre]
Maintainer: Frankie Cho <htcho@connect.hku.hk>

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Package pxweb updated to version 0.8.3 with previous version 0.6.37 dated 2018-06-12

Title: R Interface to PXWEB APIs
Description: Generic interface for the PX-Web/PC-Axis API. The PX-Web/PC-Axis API is used by organizations such as Statistics Sweden and Statistics Finland to disseminate data. The R package can interact with all PX-Web/PC-Axis APIs to fetch information about the data hierarchy, extract metadata and extract and parse statistics to R data.frame format. PX-Web is a solution to disseminate PC-Axis data files in dynamic tables on the web. Since 2013 PX-Web contains an API to disseminate PC-Axis files.
Author: Mans Magnusson [aut, cre], Love Hansson [aut], Leo Lahti [aut], Janne Huovari [ctb], Eydun Nielsen [ctb], Bo Werth [ctb], Thomas Runarsson [ctb], Torbjörn Lindquist [ctb], Palmar Thorsteinsson [ctb]
Maintainer: Mans Magnusson <mons.magnusson@gmail.com>

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Package kohonen updated to version 3.0.8 with previous version 3.0.7 dated 2018-11-01

Title: Supervised and Unsupervised Self-Organising Maps
Description: Functions to train self-organising maps (SOMs). Also interrogation of the maps and prediction using trained maps are supported. The name of the package refers to Teuvo Kohonen, the inventor of the SOM.
Author: Ron Wehrens and Johannes Kruisselbrink
Maintainer: Ron Wehrens <ron.wehrens@gmail.com>

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Package REBayes updated to version 1.4 with previous version 1.3 dated 2018-02-14

Title: Empirical Bayes Estimation and Inference
Description: Kiefer-Wolfowitz maximum likelihood estimation for mixture models and some other density estimation and regression methods based on convex optimization. See Koenker and Gu (2017) REBayes: An R Package for Empirical Bayes Mixture Methods, Journal of Statistical Software, 82, 1--26, <DOI:10.18637/jss.v082.i08>.
Author: Roger Koenker [aut, cre], Jiaying Gu [ctb], Ivan Mizera [ctb]
Maintainer: Roger Koenker <rkoenker@uiuc.edu>

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Package pinyin updated to version 1.1.5 with previous version 1.1.4 dated 2018-10-17

Title: Convert Chinese Characters into Pinyin, Sijiao, Wubi or Other Codes
Description: Convert Chinese characters into Pinyin (the official romanization system for Standard Chinese in mainland China, Malaysia, Singapore, and Taiwan. See <https://en.wikipedia.org/wiki/Pinyin> for details), Sijiao (four or five numerical digits per character. See <https://en.wikipedia.org/wiki/Four-Corner_Method>.), Wubi (an input method with five strokes. See <https://en.wikipedia.org/wiki/Wubi_method>) or user-defined codes.
Author: Peng Zhao [aut, cre], Qu Cheng [ctb]
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Sun, 16 Dec 2018

Package arulesCBA updated to version 1.1.4 with previous version 1.1.3-1 dated 2018-04-23

Title: Classification Based on Association Rules
Description: Provides a function to build an association rule-based classifier for data frames, and to classify incoming data frames using such a classifier.
Author: Ian Johnson [aut, cre, cph], Michael Hahsler [aut, cph]
Maintainer: Ian Johnson <ianjjohnson@icloud.com>

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Package spaero updated to version 0.4.0 with previous version 0.3.0 dated 2018-07-11

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>

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Package convexjlr updated to version 0.8.1 with previous version 0.7.0 dated 2018-04-28

Title: Disciplined Convex Programming in R using 'Convex.jl'
Description: Provides a simple high-level wrapper for 'Julia' package 'Convex.jl' (see <https://github.com/JuliaOpt/Convex.jl> for more information), which makes it easy to describe and solve convex optimization problems in R. The problems can be dealt with include: linear programs, second-order cone programs, semidefinite programs, exponential cone programs.
Author: Changcheng Li [aut, cre]
Maintainer: Changcheng Li <cxl508@psu.edu>

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Package rquery updated to version 1.2.1 with previous version 1.2.0 dated 2018-11-07

Title: Relational Query Generator for Data Manipulation at Scale
Description: A piped query generator based on Edgar F. Codd's relational algebra, and on production experience using 'SQL' and 'dplyr' at big data scale. The design represents an attempt to make 'SQL' more teachable by denoting composition by a sequential pipeline notation instead of nested queries or functions. The implementation delivers reliable high performance data processing on large data systems such as 'Spark', databases, and 'data.table'. Package features include: data processing trees or pipelines as observable objects (able to report both columns produced and columns used), optimized 'SQL' generation as an explicit user visible modeling step, explicit query reasoning and checking.
Author: John Mount [aut, cre], Win-Vector LLC [cph]
Maintainer: John Mount <jmount@win-vector.com>

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Package mindr updated to version 1.1.9 with previous version 1.1.5 dated 2018-10-09

Title: Convert Files Between Markdown or Rmarkdown Files and Mindmaps
Description: Convert Markdown ('.md') or Rmarkdown ('.Rmd') files into FreeMind mindmap ('.mm') files, and vice versa. FreeMind mindmap ('.mm') files can be opened by or imported to common mindmap software such as 'FreeMind' (<http://freemind.sourceforge.net/wiki/index.php/Main_Page>) and 'XMind' (<http://www.xmind.net>).
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package netCoin updated to version 0.3.2 with previous version 0.3.0 dated 2018-07-25

Title: Interactive Analytic Networks
Description: Create interactive analytic networks. It joins the data analysis power of R to obtain coincidences, co-occurrences and correlations, and the visualization libraries of 'JavaScript' in one package.
Author: Modesto Escobar <modesto@usal.es>, David Barrios <metal@usal.es>, Carlos Prieto <cprietos@usal.es>, Luis Martinez-Uribe <lmartinez@usal.es>.
Maintainer: Modesto Escobar <modesto@usal.es>

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Package wevid updated to version 0.5.2 with previous version 0.5.1 dated 2018-10-11

Title: Quantifying Performance of a Binary Classifier Through Weight of Evidence
Description: The distributions of the weight of evidence (log Bayes factor) favouring case over noncase status in a test dataset (or test folds generated by cross-validation) can be used to quantify the performance of a diagnostic test (McKeigue (2018), <doi:10.1177/0962280218776989>). The package can be used with any test dataset on which you have observed case-control status and have computed prior and posterior probabilities of case status using a model learned on a training dataset. To quantify how the predictor will behave as a risk stratifier, the quantiles of the distributions of weight of evidence in cases and controls can be calculated and plotted.
Author: Paul McKeigue [aut] (<https://orcid.org/0000-0002-5217-1034>), Marco Colombo [ctb, cre] (<https://orcid.org/0000-0001-6672-0623>)
Maintainer: Marco Colombo <mar.colombo13@gmail.com>

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Package nestfs updated to version 0.9.1 with previous version 0.9 dated 2018-09-25

Title: Cross-Validated (Nested) Forward Selection
Description: Implementation of forward selection based on cross-validated linear and logistic regression.
Author: Marco Colombo [aut, cre] (<https://orcid.org/0000-0001-6672-0623>), Felix Agakov [ctb]
Maintainer: Marco Colombo <mar.colombo13@gmail.com>

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Package cosa updated to version 1.2.1 with previous version 1.2.0 dated 2018-04-04

Title: Bound Constrained Optimal Sample Allocation
Description: Implements bound constrained optimization of sample sizes in power analysis of multilevel regression discontinuity studies (RDDs) and multilevel randomized controlled trials (RCTs) with continuous outcomes. Functions for statistical power and minimum detectable effect size calculations are also provided. Bulus, M. (2017). Design Considerations in Three-level Regression Discontinuity Studies (Doctoral dissertation). University of Missouri, Columbia, MO.
Author: Metin Bulus [aut, cre, cph], Nianbo Dong [aut, cph]
Maintainer: Metin Bulus <bulusmetin@gmail.com>

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Package bookdownplus updated to version 1.5.4 with previous version 1.5.2 dated 2018-10-16

Title: Generate Assorted Books and Documents with R 'bookdown' Package
Description: A collection and selector of R 'bookdown' templates. 'bookdownplus' helps you write academic journal articles, guitar books, chemical equations, mails, calendars, and diaries. R 'bookdownplus' extends the features of 'bookdown', and simplifies the procedure. Users only have to choose a template, clarify the book title and author name, and then focus on writing the text. No need to struggle in 'YAML' and 'LaTeX'.
Author: Peng Zhao
Maintainer: Peng Zhao <pzhao@pzhao.net>

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Package texteffect updated to version 0.2 with previous version 0.1 dated 2017-11-27

Title: Discovering Latent Treatments in Text Corpora and Estimating Their Causal Effects
Description: Implements the approach described in Fong and Grimmer (2016) <https://aclweb.org/anthology/P/P16/P16-1151.pdf> for automatically discovering latent treatments from a corpus and estimating the average marginal component effect (AMCE) of each treatment. The data is divided into a training and test set. The supervised Indian Buffet Process (sibp) is used to discover latent treatments in the training set. The fitted model is then applied to the test set to infer the values of the latent treatments in the test set. Finally, Y is regressed on the latent treatments in the test set to estimate the causal effect of each treatment.
Author: Christian Fong <christianfong@stanford.edu>
Maintainer: Christian Fong <christianfong@stanford.edu>

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Package LadR updated to version 1.0.5 with previous version 1.0.4 dated 2018-08-06

Title: Routines for Fit, Inference and Diagnostics in LAD Models
Description: LAD (Least Absolute Deviations) estimation for linear regression, confidence intervals, tests of hypotheses, methods for outliers detection, measures of leverage, methods of diagnostics for LAD regression, special diagnostics graphs and measures of leverage. The algorithms are based in Dielman (2005) <doi:10.1080/0094965042000223680>, Elian et al. (2000) <doi:10.1080/03610920008832518> and Dodge (1997) <doi:10.1006/jmva.1997.1666>. This package also has two datasets "houses" and "pollution", respectively, from Narula and Wellington (1977) <doi:10.2307/1268628> and Santos et al. (2016) <doi:10.1371/journal.pone.0163225>.
Author: Kévin Allan Sales Rodrigues <kevin.asr@outlook.com>
Maintainer: Kevin Allan Sales Rodrigues <kevin.asr@outlook.com>

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Sat, 15 Dec 2018

Package schoRsch updated to version 1.5 with previous version 1.4 dated 2017-02-14

Title: Tools for Analyzing Factorial Experiments
Description: Offers a helping hand to psychologists and other behavioral scientists who routinely deal with experimental data from factorial experiments. It includes several functions to format output from other R functions according to the style guidelines of the APA (American Psychological Association). This formatted output can be copied directly into manuscripts to facilitate data reporting. These features are backed up by a toolkit of several small helper functions, e.g., offering out-of-the-box outlier removal. The package lends its name to Georg "Schorsch" Schuessler, ingenious technician at the Department of Psychology III, University of Wuerzburg. For details on the implemented methods, see Roland Pfister and Markus Janczyk (2016) <doi: 10.20982/tqmp.12.2.p147>.
Author: Roland Pfister, Markus Janczyk
Maintainer: Roland Pfister <roland.pfister@psychologie.uni-wuerzburg.de>

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Package foolbox updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-27

Title: Function Manipulation Toolbox
Description: Provides functionality for manipulating functions and translating them in metaprogramming.
Author: Thomas Mailund [aut, cre]
Maintainer: Thomas Mailund <mailund@birc.au.dk>

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Package conf updated to version 1.5.0 with previous version 1.4.0 dated 2018-11-02

Title: Visualization and Analysis of Statistical Measures of Confidence
Description: Enables: (1) plotting two-dimensional confidence regions, (2) coverage analysis of confidence region simulations and (3) calculating confidence intervals and the associated actual coverage for binomial proportions. Each is given in greater detail next. (1) Plots the two-dimensional confidence region for probability distribution parameters (supported distribution suffixes: cauchy, gamma, invgauss, logis, llogis, lnorm, norm, unif, weibull) corresponding to a user-given complete or right-censored dataset and level of significance. The crplot() algorithm plots more points in areas of greater curvature to ensure a smooth appearance throughout the confidence region boundary. An alternative heuristic plots a specified number of points at roughly uniform intervals along its boundary. Both heuristics build upon the radial profile log-likelihood ratio technique for plotting confidence regions given by Jaeger (2016) <doi:10.1080/00031305.2016.1182946>. (2) Performs confidence region coverage simulations for a random sample drawn from a user- specified parametric population distribution, or for a user-specified dataset and point of interest with coversim(). (3) Calculates confidence interval bounds for a binomial proportion with binomTest(), calculates the actual coverage with binomTestCoverage(), and plots the actual coverage with binomTestCoveragePlot(). Calculates confidence interval bounds for the binomial proportion using an ensemble of constituent confidence intervals with binomTestEnsemble().
Author: Christopher Weld [aut, cre] (<https://orcid.org/0000-0001-5902-9738>), Hayeon Park [aut], Lawrence Leemis [aut], Andrew Loh [ctb], Yuan Chang [ctb], Brock Crook [ctb], Xin Zhang [ctb]
Maintainer: Christopher Weld <ceweld@email.wm.edu>

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Package AdvDif4 updated to version 0.4.18 with previous version 0.3.18 dated 2018-09-13

Title: Solving 1D Advection Bi-Flux Diffusion Equation
Description: This software solves an Advection Bi-Flux Diffusive Problem using the Finite Difference Method FDM. Vasconcellos, J.F.V., Marinho, G.M., Zanni, J.H., 2016, Numerical analysis of an anomalous diffusion with a bimodal flux distribution. <doi:10.1016/j.rimni.2016.05.001>. Silva, L.G., Knupp, D.C., Bevilacqua, L., Galeao, A.C.N.R., Silva Neto, A.J., 2014, Formulation and solution of an Inverse Anomalous Diffusion Problem with Stochastic Techniques. <doi:10.5902/2179460X13184>. In this version, it is possible to include a source as a function depending on space and time, that is, s(x,t).
Author: Jader Lugon Junior, Pedro Paulo Gomes Watts Rodrigues, Luiz Bevilacqua, Gisele Moraes Marinho, Diego Campos Knupp, Joao Flavio Vieira Vasconcellos and Antonio Jose da Silva Neto.
Maintainer: Jader Lugon Junior <jlugonjr@gmail.com>

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Package redist updated to version 1.3-3 with previous version 1.3-2 dated 2018-10-17

Title: Markov Chain Monte Carlo Methods for Redistricting Simulation
Description: Enables researchers to sample redistricting plans from a pre- specified target distribution using a Markov Chain Monte Carlo algorithm. The package allows for the implementation of various constraints in the redistricting process such as geographic compactness and population parity requirements. The algorithm also can be used in combination with efficient simulation methods such as simulated and parallel tempering algorithms. Tools for analysis such as inverse probability reweighting and plotting functionality are included. The package implements methods described in Fifield, Higgins, Imai and Tarr (2016) ``A New Automated Redistricting Simulator Using Markov Chain Monte Carlo,'' working paper available at <https://imai.fas.harvard.edu/research/files/redist.pdf>.
Author: Ben Fifield <bfifield@princeton.edu>, Alexander Tarr <atarr@princeton.edu>, Michael Higgins <mikehiggins@k-state.edu>, and Kosuke Imai <imai@harvard.edu>
Maintainer: Ben Fifield <bfifield@princeton.edu>

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Package MHTdiscrete updated to version 1.0.1 with previous version 1.0.0 dated 2017-11-23

Title: Multiple Hypotheses Testing for Discrete Data
Description: A comprehensive tool for almost all existing multiple testing methods for discrete data. The package also provides some novel multiple testing procedures controlling FWER/FDR for discrete data. Given discrete p-values and their domains, the [method].p.adjust function returns adjusted p-values, which can be used to compare with the nominal significant level alpha and make decisions. For users' convenience, the functions also provide the output option for printing decision rules.
Author: Yalin Zhu, Wenge Guo
Maintainer: Yalin Zhu <yalin.zhu@outlook.com>

Diff between MHTdiscrete versions 1.0.0 dated 2017-11-23 and 1.0.1 dated 2018-12-15

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Package QuantumOps updated to version 2.0 with previous version 1.0 dated 2018-11-19

Title: Performs Common Linear Algebra Operations Used in Quantum Computing
Description: Contains basic structures and operations used frequently in quantum computing. Intended to be a convenient tool to help in practicing the linear algebra involved in quantum operations. Has functionality for the creation of arbitrarily sized kets, bras, matrices and implements quantum gates, inner products, and tensor products. Can convert functions into equivalent quantum gates.
Author: Salonik Resch
Maintainer: Salonik Resch <resc0059@umn.edu>

Diff between QuantumOps versions 1.0 dated 2018-11-19 and 2.0 dated 2018-12-15

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Permanent link

Package pillar updated to version 1.3.1 with previous version 1.3.0 dated 2018-07-14

Title: Coloured Formatting for Columns
Description: Provides a 'pillar' generic designed for formatting columns of data using the full range of colours provided by modern terminals.
Author: Kirill Müller [aut, cre], Hadley Wickham [aut], RStudio [cph]
Maintainer: Kirill Müller <krlmlr+r@mailbox.org>

Diff between pillar versions 1.3.0 dated 2018-07-14 and 1.3.1 dated 2018-12-15

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More information about pillar at CRAN
Permanent link

Package hunspell updated to version 3.0 with previous version 2.9 dated 2017-12-16

Title: High-Performance Stemmer, Tokenizer, and Spell Checker
Description: Low level spell checker and morphological analyzer based on the famous 'hunspell' library <https://hunspell.github.io>. The package can analyze or check individual words as well as parse text, latex, html or xml documents. For a more user-friendly interface use the 'spelling' package which builds on this package to automate checking of files, documentation and vignettes in all common formats.
Author: Jeroen Ooms [aut, cre], Authors of libhunspell [cph] (see AUTHORS file)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Permanent link

Package rscala updated to version 3.2.6 with previous version 3.2.5 dated 2018-12-08

Title: Bridge Between 'R' and 'Scala' with Callbacks
Description: 'Scala' <http://www.scala-lang.org/> is embedded in 'R' and callbacks from 'Scala' to 'R' are available. Support is provided to write 'R' packages that access 'Scala'. After installation, please run 'rscala::scalaConfig()'.
Author: David B. Dahl [aut, cre]
Maintainer: David B. Dahl <dahl@stat.byu.edu>

Diff between rscala versions 3.2.5 dated 2018-12-08 and 3.2.6 dated 2018-12-15

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Permanent link

Package ragtop updated to version 1.0.0 with previous version 0.5 dated 2016-09-28

Title: Pricing Equity Derivatives with Extensions of Black-Scholes
Description: Algorithms to price American and European equity options, convertible bonds and a variety of other financial derivatives. It uses an extension of the usual Black-Scholes model in which jump to default may occur at a probability specified by a power-law link between stock price and hazard rate as found in the paper by Takahashi, Kobayashi, and Nakagawa (2001) <doi:10.3905/jfi.2001.319302>. We use ideas and techniques from Andersen and Buffum (2002) <doi:10.2139/ssrn.355308> and Linetsky (2006) <doi:10.1111/j.1467-9965.2006.00271.x>.
Author: Brian K. Boonstra
Maintainer: Brian K. Boonstra <ragtop@boonstra.org>

Diff between ragtop versions 0.5 dated 2016-09-28 and 1.0.0 dated 2018-12-15

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Package psda updated to version 1.2.0 with previous version 1.0.1 dated 2018-10-08

Title: Polygonal Symbolic Data Analysis
Description: An implementation of symbolic polygonal data analysis. The package presents the estimation of main descriptive statistical measures, e.g, mean, covariance, variance, correlation and coefficient of variation. In addition, transformation of the data in polygons. Empirical probability distribution function based on polygonal histogram and regression models are presented.
Author: Wagner Silva [aut, cre, ths], Renata Souza [aut], Francisco Cysneiros [aut]
Maintainer: Wagner Silva <wjfs@cin.ufpe.br>

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Package GMCM updated to version 1.3.0 with previous version 1.2.4 dated 2017-01-13

Title: Fast Estimation of Gaussian Mixture Copula Models
Description: Unsupervised Clustering and Meta-analysis using Gaussian Mixture Copula Models.
Author: Anders Ellern Bilgrau, Martin Boegsted, Poul Svante Eriksen
Maintainer: Anders Ellern Bilgrau <anders.ellern.bilgrau@gmail.com>

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Package WordPools updated to version 1.1-1 with previous version 1.0-2 dated 2012-12-16

Title: Classical Word Pools Used in Studies of Learning and Memory
Description: Collects several classical word pools used most often to provide lists of words in psychological studies of learning and memory. It provides a simple function, 'pickList' for selecting random samples of words within given ranges.
Author: Michael Friendly [aut, cre] (<https://orcid.org/0000-0002-3237-0941>)
Maintainer: Michael Friendly <friendly@yorku.ca>

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Package linl updated to version 0.0.3 with previous version 0.0.2 dated 2017-10-29

Title: 'linl' is not 'Letter'
Description: A 'LaTeX' Letter class for 'rmarkdown', using the 'pandoc-letter' template adapted for use with 'markdown'.
Author: Dirk Eddelbuettel and Aaron Wolen
Maintainer: Dirk Eddelbuettel <edd@debian.org>

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Package PowerUpR updated to version 1.0.2 with previous version 1.0.1 dated 2018-10-18

Title: Power Analysis Tools for Multilevel Randomized Experiments
Description: Includes tools to calculate statistical power, minimum detectable effect size, and minimum required sample size for various multilevel randomized experiments with continuous outcomes. Some of the functions can assist with planning two- and three-level cluster-randomized trials (CRTs) sensitive to moderation effects, and with planning two-level CRTs sensitive to 2-2-1 and 2-1-1 mediation effects. See 'PowerUp!' Excel series at <https://www.causalevaluation.org/>.
Author: Metin Bulus [aut, cre], Nianbo Dong [aut], Benjamin Kelcey [aut], Jessaca Spybrook [aut]
Maintainer: Metin Bulus <bulusmetin@gmail.com>

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Package iNEXT updated to version 2.0.18 with previous version 2.0.17 dated 2018-09-19

Title: Interpolation and Extrapolation for Species Diversity
Description: Provides simple functions to compute and plot two types (sample-size- and coverage-based) rarefaction and extrapolation of species diversity (Hill numbers) for individual-based (abundance) data or sampling-unit- based (incidence) data.
Author: T. C. Hsieh, K. H. Ma and Anne Chao
Maintainer: T. C. Hsieh <euler96@gmail.com>

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Package spacyr updated to version 1.0 with previous version 0.9.91 dated 2018-07-16

Title: Wrapper to the 'spaCy' 'NLP' Library
Description: An R wrapper to the 'Python' 'spaCy' 'NLP' library, from <http://spacy.io>.
Author: Kenneth Benoit [cre, aut, cph] (<https://orcid.org/0000-0002-0797-564X>), Akitaka Matsuo [aut] (<https://orcid.org/0000-0002-3323-6330>), European Research Council [fnd] (ERC-2011-StG 283794-QUANTESS)
Maintainer: Kenneth Benoit <kbenoit@lse.ac.uk>

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Fri, 14 Dec 2018

Package bold updated to version 0.8.6 with previous version 0.8.0 dated 2018-10-26

Title: Interface to Bold Systems API
Description: A programmatic interface to the Web Service methods provided by Bold Systems (<http://www.boldsystems.org/>) for genetic 'barcode' data. Functions include methods for searching by sequences by taxonomic names, ids, collectors, and institutions; as well as a function for searching for specimens, and downloading trace files.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package ggspatial updated to version 1.0.3 with previous version 1.0.2 dated 2018-10-27

Title: Spatial Data Framework for ggplot2
Description: Spatial data plus the power of the ggplot2 framework means easier mapping when input data are already in the form of spatial objects.
Author: Dewey Dunnington [aut, cre] (<https://orcid.org/0000-0002-9415-4582>), Brent Thorne [ctb]
Maintainer: Dewey Dunnington <dewey@fishandwhistle.net>

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Package bezier updated to version 1.1.2 with previous version 1.1 dated 2014-07-18

Title: Toolkit for Bezier Curves and Splines
Description: The bezier package is a toolkit for working with Bezier curves and splines. The package provides functions for point generation, arc length estimation, degree elevation and curve fitting.
Author: Aaron Olsen
Maintainer: Aaron Olsen <aarolsen@gmail.com>

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Package rglobi updated to version 0.2.17 with previous version 0.2.14 dated 2018-03-23

Title: R Interface to Global Biotic Interactions
Description: A programmatic interface to the web service methods provided by Global Biotic Interactions (GloBI). GloBI provides access to spatial-temporal species interaction records from sources all over the world. rglobi provides methods to search species interactions by location, interaction type, and taxonomic name. In addition, it supports Cypher, a graph query language, to allow for executing custom queries on the GloBI aggregate species interaction data set.
Author: Jorrit Poelen [aut, cre], Stephen Gosnell [aut], Sergey Slyusarev [aut]
Maintainer: Jorrit Poelen <jhpoelen@xs4all.nl>

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Package TPMplt updated to version 0.1.2 with previous version 0.1.1 dated 2018-12-02

Title: Tool-Kit for Dynamic Materials Model and Thermal Processing Maps
Description: Provides a simple approach for constructing dynamic materials modeling suggested by Prasad and Gegel <doi:10.1007/BF02664902>. It can easily generate various processing-maps based on this model as well. The calculation result in this package contains full materials constants, information about power dissipation efficiency factor, and rheological properties, can be exported completely also, through which further analysis and customized plots will be applicable as well.
Author: ZHANG_Chen Developer [aut, com, cre]
Maintainer: ZHANG_Chen Developer <447974102@qq.com>

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Package RTest updated to version 1.2.2 with previous version 1.2.1 dated 2018-12-11

Title: A XML-Based Testing Framework for Automated Component Tests of R Packages
Description: This provides a framework for R packages developed for a regulatory environment. It is based on the 'testthat' unit testing system and provides the adapter functionalities for XML-based test case definition as well as for standardized reporting of the test results.
Author: Sebastian Wolf [aut, cre], Matthias Pfeifer [aut, ctb], Sergej Potapov [ctb], Roche [cph, fnd]
Maintainer: Sebastian Wolf <sebastian@mail-wolf.de>

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Package msaenet updated to version 3.0 with previous version 2.9 dated 2018-05-14

Title: Multi-Step Adaptive Estimation Methods for Sparse Regressions
Description: Multi-step adaptive elastic-net (MSAENet) algorithm for feature selection in high-dimensional regressions proposed in Xiao and Xu (2015) <DOI:10.1080/00949655.2015.1016944>, with support for multi-step adaptive MCP-net (MSAMNet) and multi-step adaptive SCAD-net (MSASNet) methods.
Author: Nan Xiao [aut, cre] (<https://orcid.org/0000-0002-0250-5673>), Qing-Song Xu [aut]
Maintainer: Nan Xiao <me@nanx.me>

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Package ConvergenceClubs updated to version 1.4.3 with previous version 1.4.2 dated 2018-12-06

Title: Finding Convergence Clubs
Description: Functions for clustering regions that form convergence clubs, according to the definition of Phillips and Sul (2009) <doi:10.1002/jae.1080>.
Author: Roberto Sichera [aut, cre, cph], Pietro Pizzuto [aut]
Maintainer: Roberto Sichera <roberto.sichera@unipa.it>

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Package tweenr updated to version 1.0.1 with previous version 1.0.0 dated 2018-09-27

Title: Interpolate Data for Smooth Animations
Description: In order to create smooth animation between states of data, tweening is necessary. This package provides a range of functions for creating tweened data that can be used as basis for animation. Furthermore it adds a number of vectorized interpolaters for common R data types such as numeric, date and colour.
Author: Thomas Lin Pedersen [aut, cre]
Maintainer: Thomas Lin Pedersen <thomasp85@gmail.com>

Diff between tweenr versions 1.0.0 dated 2018-09-27 and 1.0.1 dated 2018-12-14

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Package Rcan updated to version 1.3.63 with previous version 1.3.62 dated 2018-12-10

Title: Cancer Registry Data Analysis and Visualisation
Description: Tools for basic and advance cancer statistics and graphics. Calculates age-specific rate, age-standardized rate, estimated annual percentage rate with standards error. Creates graphics across variable and time, such as age-specific trends and period-cohort trends.
Author: Mathieu Laversanne [aut, cre], Cancer Surveillance Unit [cph]
Maintainer: Mathieu Laversanne <laversannem@iarc.fr>

Diff between Rcan versions 1.3.62 dated 2018-12-10 and 1.3.63 dated 2018-12-14

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Package multinet updated to version 2.0.1 with previous version 2.0.0 dated 2018-12-06

Title: Analysis and Mining of Multilayer Social Networks
Description: Functions for the creation/generation and analysis of multilayer social networks.
Author: Matteo Magnani, Davide Vega, Mikael Dubik (glouvain). The package uses functions from eclat (www.borgelt.net/eclat.html), for association rule mining, Eigen (eigen.tuxfamily.org) and spectra (https://spectralib.org), for matrix manipulation, Infomap (www.mapequation.org), for the Infomap community detection method, and Howard Hinnant's date and time library (https://github.com/HowardHinnant/date). The code from this libraries has been included in our source package.
Maintainer: Matteo Magnani <matteo.magnani@it.uu.se>

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Package minerva updated to version 1.5 with previous version 1.4.7 dated 2017-07-21

Title: Maximal Information-Based Nonparametric Exploration for Variable Analysis
Description: Wrapper for 'minepy' implementation of Maximal Information-based Nonparametric Exploration statistics (MIC and MINE family). Detailed information of the ANSI C implementation of 'minepy' can be found at <http://minepy.readthedocs.io/en/latest>.
Author: Michele Filosi [aut, cre], Roberto Visintainer [aut], Davide Albanese [aut], Samantha Riccadonna [ctb], Giuseppe Jurman [ctb], Cesare Furlanello [ctb]
Maintainer: Michele Filosi <michele.filosi@gmail.com>

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Package detpack updated to version 1.1.2 with previous version 1.1.1 dated 2018-04-26

Title: Density Estimation and Random Number Generation with Distribution Element Trees
Description: Density estimation for possibly large data sets and conditional/unconditional random number generation or bootstrapping with distribution element trees. The function 'det.construct' translates a dataset into a distribution element tree. To evaluate the probability density based on a previously computed tree at arbitrary query points, the function 'det.query' is available. The functions 'det1' and 'det2' provide density estimation and plotting for one- and two-dimensional datasets. Conditional/unconditional smooth bootstrapping from an available distribution element tree can be performed by 'det.rnd'. For more details on distribution element trees, see: Meyer, D.W. (2016) <arXiv:1610.00345> or Meyer, D.W., Statistics and Computing (2017) <doi:10.1007/s11222-017-9751-9> and Meyer, D.W. (2017) <arXiv:1711.04632> or Meyer, D.W., Journal of Computational and Graphical Statistics (2018) <doi:10.1080/10618600.2018.1482768>.
Author: Daniel Meyer
Maintainer: Daniel Meyer <meyerda@ethz.ch>

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Package blorr updated to version 0.2.0 with previous version 0.1.0 dated 2018-05-11

Title: Tools for Developing Binary Logistic Regression Models
Description: Tools designed to make it easier for beginner and intermediate users to build and validate binary logistic regression models. Includes bivariate analysis, comprehensive regression output, model fit statistics, variable selection procedures, model validation techniques and a 'shiny' app for interactive model building.
Author: Aravind Hebbali [aut, cre] (<https://orcid.org/0000-0001-9220-9669>)
Maintainer: Aravind Hebbali <hebbali.aravind@gmail.com>

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Package TraMineRextras updated to version 0.4.4 with previous version 0.4.3 dated 2018-08-22

Title: TraMineR Extension
Description: Collection of ancillary functions and utilities to be used in conjunction with the 'TraMineR' package for sequence data exploration. Most of the functions are in test phase, lack systematic consistency check of the arguments and are subject to changes. Once fully checked, some of the functions of this collection could be included in a next release of 'TraMineR'.
Author: Gilbert Ritschard [aut, cre, ths, cph], Matthias Studer [aut], Reto Buergin [aut], Alexis Gabadinho [ctb], Pierre-Alexandre Fonta [ctb], Nicolas Muller [ctb], Patrick Rousset [ctb]
Maintainer: Gilbert Ritschard <gilbert.ritschard@unige.ch>

Diff between TraMineRextras versions 0.4.3 dated 2018-08-22 and 0.4.4 dated 2018-12-14

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Package backports updated to version 1.1.3 with previous version 1.1.2 dated 2017-12-13

Title: Reimplementations of Functions Introduced Since R-3.0.0
Description: Functions introduced or changed since R v3.0.0 are re-implemented in this package. The backports are conditionally exported in order to let R resolve the function name to either the implemented backport, or the respective base version, if available. Package developers can make use of new functions or arguments by selectively importing specific backports to support older installations.
Author: Michel Lang [cre, aut] (<https://orcid.org/0000-0001-9754-0393>), R Core Team [aut]
Maintainer: Michel Lang <michellang@gmail.com>

Diff between backports versions 1.1.2 dated 2017-12-13 and 1.1.3 dated 2018-12-14

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Package RSA updated to version 0.9.13 with previous version 0.9.12 dated 2018-07-03

Title: Response Surface Analysis
Description: Advanced response surface analysis. The main function RSA computes and compares several nested polynomial regression models (full polynomial, shifted and rotated squared differences, rising ridge surfaces, basic squared differences). The package provides plotting functions for 3d wireframe surfaces, interactive 3d plots, and contour plots. Calculates many surface parameters (a1 to a4, principal axes, stationary point, eigenvalues) and provides standard, robust, or bootstrapped standard errors and confidence intervals for them.
Author: Felix Schönbrodt [cre, aut], Sarah Humberg [aut]
Maintainer: Felix Schönbrodt <felix@nicebread.de>

Diff between RSA versions 0.9.12 dated 2018-07-03 and 0.9.13 dated 2018-12-14

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Package RefFreeEWAS updated to version 2.2 with previous version 2.1 dated 2017-02-25

Title: EWAS using Reference-Free DNA Methylation Mixture Deconvolution
Description: Reference-free method for conducting EWAS while deconvoluting DNA methylation arising as mixtures of cell types. The older method (Houseman et al., 2014,<doi:10.1093/bioinformatics/btu029>) is similar to surrogate variable analysis (SVA and ISVA), except that it makes additional use of a biological mixture assumption. The newer method (Houseman et al., 2016, <doi:10.1186/s12859-016-1140-4>) is similar to non-negative matrix factorization, with additional constraints and additional utilities.
Author: E. Andres Houseman, Sc.D.
Maintainer: E. Andres Houseman <eahouseman@gmail.com>

Diff between RefFreeEWAS versions 2.1 dated 2017-02-25 and 2.2 dated 2018-12-14

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Package pgmm updated to version 1.2.3 with previous version 1.2.2 dated 2018-03-18

Title: Parsimonious Gaussian Mixture Models
Description: Carries out model-based clustering or classification using parsimonious Gaussian mixture models. McNicholas and Murphy (2008) <doi:10.1007/s11222-008-9056-0>, McNicholas (2010) <doi:10.1016/j.jspi.2009.11.006>, McNicholas and Murphy (2010) <doi:10.1093/bioinformatics/btq498>, McNicholas et al. (2010) <doi:10.1016/j.csda.2009.02.011>.
Author: Paul D. McNicholas [aut, cre], Aisha ElSherbiny [aut], K. Raju Jampani [ctb], Aaron F. McDaid [aut], T. Brendan Murphy [aut], Larry Banks [ctb]
Maintainer: Paul D. McNicholas <mcnicholas@math.mcmaster.ca>

Diff between pgmm versions 1.2.2 dated 2018-03-18 and 1.2.3 dated 2018-12-14

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Package Ball updated to version 1.3.7 with previous version 1.3.6 dated 2018-12-03

Title: Statistical Inference and Sure Independence Screening via Ball Statistics
Description: Hypothesis tests and sure independence screening (SIS) procedure based on ball statistics, including ball divergence <doi:10.1214/17-AOS1579>, ball covariance, and ball correlation <doi:10.1080/01621459.2018.1462709>, are developed to analyze complex data. The ball divergence and ball covariance based distribution-free tests are implemented to detecting distribution difference and association in metric spaces <arXiv:1811.03750>. Furthermore, a generic non-parametric SIS procedure based on ball correlation and all of its variants are implemented to tackle the challenge in the context of ultra high dimensional data.
Author: Xueqin Wang, Wenliang Pan, Heping Zhang, Hongtu Zhu, Yuan Tian, Weinan Xiao, Chengfeng Liu, Jin Zhu
Maintainer: Jin Zhu <zhuj37@mail2.sysu.edu.cn>

Diff between Ball versions 1.3.6 dated 2018-12-03 and 1.3.7 dated 2018-12-14

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Thu, 13 Dec 2018

Package STARTS updated to version 1.1-6 with previous version 1.0-6 dated 2018-12-12

Title: Functions for the STARTS Model
Description: Contains functions for estimating the STARTS model of Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>, <DOI:10.1037/10409-008>. Penalized maximum likelihood estimation and Markov Chain Monte Carlo estimation are also provided, see Luedtke, Robitzsch and Wagner (2018) <DOI:10.1037/met0000155>.
Author: Alexander Robitzsch [aut,cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between STARTS versions 1.0-6 dated 2018-12-12 and 1.1-6 dated 2018-12-13

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Package pomp updated to version 1.19 with previous version 1.18 dated 2018-07-09

Title: Statistical Inference for Partially Observed Markov Processes
Description: Tools for working with partially observed Markov process (POMP) models (also known as stochastic dynamical systems, hidden Markov models, and nonlinear, non-Gaussian, state-space models). The package provides facilities for implementing POMP models, simulating them, and fitting them to time series data by a variety of frequentist and Bayesian methods. It is also a versatile platform for implementation of inference methods for general POMP models.
Author: Aaron A. King [aut, cre], Edward L. Ionides [aut], Carles Breto [aut], Stephen P. Ellner [ctb], Matthew J. Ferrari [ctb], Bruce E. Kendall [ctb], Michael Lavine [ctb], Dao Nguyen [ctb], Daniel C. Reuman [ctb], Helen Wearing [ctb], Simon N. Wood [ctb], Sebastian Funk [ctb], Steven G. Johnson [ctb], Eamon O'Dea [ctb]
Maintainer: Aaron A. King <kingaa@umich.edu>

Diff between pomp versions 1.18 dated 2018-07-09 and 1.19 dated 2018-12-13

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Package HCmodelSets updated to version 1.0.1 with previous version 1.0.0 dated 2018-12-11

Title: Regression with a Large Number of Potential Explanatory Variables
Description: Software for performing the reduction, exploratory and model selection phases of the procedure proposed by Cox, D.R. and Battey, H.S. (2017) <doi:10.1073/pnas.1703764114> for sparse regression when the number of potential explanatory variables far exceeds the sample size. The software supports linear regression, likelihood-based fitting of generalized linear regression models and the proportional hazards model fitted by partial likelihood.
Author: H. H. Hoeltgebaum
Maintainer: H. H. Hoeltgebaum <hh3015@ic.ac.uk>

Diff between HCmodelSets versions 1.0.0 dated 2018-12-11 and 1.0.1 dated 2018-12-13

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Package hBayesDM updated to version 0.7.0 with previous version 0.6.0 dated 2018-09-11

Title: Hierarchical Bayesian Modeling of Decision-Making Tasks
Description: Fit an array of decision-making tasks with computational models in a hierarchical Bayesian framework. Can perform hierarchical Bayesian analysis of various computational models with a single line of coding.
Author: Woo-Young Ahn [aut, cre], Nate Haines [aut], Lei Zhang [aut], Harhim Park [ctb], Jaeyeong Yang [ctb], Jethro Lee [ctb]
Maintainer: Woo-Young Ahn <wooyoung.ahn@gmail.com>

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Package fst updated to version 0.8.10 with previous version 0.8.8 dated 2018-06-07

Title: Lightning Fast Serialization of Data Frames for R
Description: Multithreaded serialization of compressed data frames using the 'fst' format. The 'fst' format allows for random access of stored data and compression with the LZ4 and ZSTD compressors created by Yann Collet. The ZSTD compression library is owned by Facebook Inc.
Author: Mark Klik [aut, cre, cph], Yann Collet [ctb, cph] (Yann Collet is author of the bundled LZ4 and ZSTD code and copyright holder of LZ4), Facebook, Inc. [cph] (Bundled ZSTD code)
Maintainer: Mark Klik <markklik@gmail.com>

Diff between fst versions 0.8.8 dated 2018-06-07 and 0.8.10 dated 2018-12-13

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Package emmeans updated to version 1.3.1 with previous version 1.3.0 dated 2018-10-26

Title: Estimated Marginal Means, aka Least-Squares Means
Description: Obtain estimated marginal means (EMMs) for many linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and compact letter displays. Least-squares means are discussed, and the term "estimated marginal means" is suggested, in Searle, Speed, and Milliken (1980) Population marginal means in the linear model: An alternative to least squares means, The American Statistician 34(4), 216-221 <doi:10.1080/00031305.1980.10483031>.
Author: Russell Lenth [aut, cre, cph], Henrik Singmann [ctb], Jonathon Love [ctb], Paul Buerkner [ctb], Maxime Herve [ctb]
Maintainer: Russell Lenth <russell-lenth@uiowa.edu>

Diff between emmeans versions 1.3.0 dated 2018-10-26 and 1.3.1 dated 2018-12-13

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Permanent link

Package dynamac updated to version 0.1.6 with previous version 0.1.5 dated 2018-12-08

Title: Dynamic Simulation and Testing for Single-Equation ARDL Models
Description: While autoregressive distributed lag (ARDL) models allow for extremely flexible dynamics, interpreting substantive significance of complex lag structures remains difficult. This package is designed to assist users in dynamically simulating and plotting the results of various ARDL models. It also contains post-estimation diagnostics, including a test for cointegration when estimating the error-correction variant of the autoregressive distributed lag model (Pesaran, Shin, and Smith 2001 <doi:10.1002/jae.616>).
Author: Soren Jordan [aut, cre, cph], Andrew Q. Philips [aut]
Maintainer: Soren Jordan <sorenjordanpols@gmail.com>

Diff between dynamac versions 0.1.5 dated 2018-12-08 and 0.1.6 dated 2018-12-13

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Package msBP updated to version 1.4 with previous version 1.3-1 dated 2017-09-04

Title: Multiscale Bernstein Polynomials for Densities
Description: Performs Bayesian nonparametric multiscale density estimation and multiscale testing of group differences with multiscale Bernstein polynomials (msBP) mixtures as in Canale and Dunson (2016).
Author: Antonio Canale
Maintainer: Antonio Canale <canale@stat.unipd.it>

Diff between msBP versions 1.3-1 dated 2017-09-04 and 1.4 dated 2018-12-13

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Package hmi updated to version 0.9.15 with previous version 0.9.13 dated 2018-06-01

Title: Hierarchical Multiple Imputation
Description: Runs single level and multilevel imputation models. The user just has to pass the data to the main function and, optionally, his analysis model. Basically the package then translates this analysis model into commands to impute the data according to it with functions from 'mice', 'MCMCglmm' or routines build for this package.
Author: Matthias Speidel [aut, cre] (Institute for Employment Research, Nuremberg, Germany), Joerg Drechsler [aut] (Institute for Employment Research, Nuremberg, Germany), Shahab Jolani [aut] (Maastricht University, Maastricht, The Netherlands)
Maintainer: Matthias Speidel <matthias.speidel@googlemail.com>

Diff between hmi versions 0.9.13 dated 2018-06-01 and 0.9.15 dated 2018-12-13

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Package datetime updated to version 0.1.4 with previous version 0.1.3 dated 2018-03-17

Title: Nominal Dates, Times, and Durations
Description: Provides methods for working with nominal dates, times, and durations. Base R has sophisticated facilities for handling time, but these can give unexpected results if, for example, timezone is not handled properly. This package provides a more casual approach to support cases which do not require rigorous treatment. It systematically deconstructs the concepts origin and timezone, and de-emphasizes the display of seconds. It also converts among nominal durations such as seconds, hours, days, and weeks. See '?datetime' and '?duration' for examples. Adapted from 'metrumrg' <http://r-forge.r-project.org/R/?group_id=1215>.
Author: Tim Bergsma
Maintainer: Tim Bergsma <bergsmat@gmail.com>

Diff between datetime versions 0.1.3 dated 2018-03-17 and 0.1.4 dated 2018-12-13

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Package photobiologyInOut updated to version 0.4.19 with previous version 0.4.18 dated 2018-11-24

Title: Read Spectral and Logged Data from Foreign Files
Description: Functions for reading, and in some cases writing, foreign files containing spectral data from spectrometers and their associated software, output from daylight simulation models in common use, and some spectral data repositories. As well as functions for exchange of spectral data with other R packages. Part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

Diff between photobiologyInOut versions 0.4.18 dated 2018-11-24 and 0.4.19 dated 2018-12-13

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Package RSuite updated to version 0.34-248 with previous version 0.33-246 dated 2018-09-25

Title: Supports Developing, Building and Deploying R Solution
Description: Supports safe and reproducible solutions development in R. It will help you with environment separation per project, dependency management, local packages creation and preparing deployment packs for your solutions.
Author: Walerian Sokolowski [aut, cre], Wit Jakuczun [aut], Yulia Yakimechko [aut], Mateusz Kalinowski [aut], Ryszard Szymanski [aut], WLOG Solutions [cph], R Consortium [ctb] (Definitions of system requirements are taken from sysreqsdb project.)
Maintainer: Walerian Sokolowski <rsuite@wlogsolutions.com>

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Package scclust updated to version 0.2.2 with previous version 0.2.1 dated 2018-12-12

Title: Size-Constrained Clustering
Description: Provides wrappers for 'scclust', a C library for computationally efficient size-constrained clustering with near-optimal performance. See <https://github.com/fsavje/scclust> for more information.
Author: Fredrik Savje [aut, cre], Michael Higgins [aut], Jasjeet Sekhon [aut]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between scclust versions 0.2.1 dated 2018-12-12 and 0.2.2 dated 2018-12-13

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Package Rlda updated to version 0.2.6 with previous version 0.2.5 dated 2018-07-13

Title: Bayesian LDA for Mixed-Membership Clustering Analysis
Description: Estimates the Bayesian LDA model for mixed-membership clustering based on different types of data (i.e., Multinomial, Bernoulli, and Binomial entries). Albuquerque, Valle and Li (2019) <doi:10.1016/j.knosys.2018.10.024>.
Author: Pedro Albuquerque and Denis Valle and Daijiang Li
Maintainer: Pedro Albuquerque <pedroa@unb.br>

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Package Partiallyoverlapping updated to version 2.0 with previous version 1.1 dated 2018-12-10

Title: Partially Overlapping Samples Tests
Description: Tests for a comparison of two partially overlapping samples. A comparison of means using the partially overlapping samples t-test: See Derrick, Russ, Toher and White (2017), Test statistics for the comparison of means for two samples which include both paired observations and independent observations, Journal of Modern Applied Statistical Methods, 16(1). A comparison of proportions using the partially overlapping samples z-test: See Derrick, Dobson-Mckittrick, Toher and White (2015), Test statistics for comparing two proportions with partially overlapping samples. Journal of Applied Quantitative Methods, 10(3).
Author: Ben Derrick
Maintainer: Ben Derrick <ben.derrick@uwe.ac.uk>

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Package CDM updated to version 7.1-20 with previous version 7.0-12 dated 2018-11-06

Title: Cognitive Diagnosis Modeling
Description: Functions for cognitive diagnosis modeling and multidimensional item response modeling for dichotomous and polytomous item responses. This package enables the estimation of the DINA and DINO model (Junker & Sijtsma, 2001, <doi:10.1177/01466210122032064>), the multiple group (polytomous) GDINA model (de la Torre, 2011, <doi:10.1007/s11336-011-9207-7>), the multiple choice DINA model (de la Torre, 2009, <doi:10.1177/0146621608320523>), the general diagnostic model (GDM; von Davier, 2008, <doi:10.1348/000711007X193957>), the structured latent class model (SLCA; Formann, 1992, <doi:10.1080/01621459.1992.10475229>) and regularized latent class analysis (Chen, Li, Liu, & Ying, 2017, <doi:10.1007/s11336-016-9545-6>). See George, Robitzsch, Kiefer, Gross, and Uenlue (2017) <doi:10.18637/jss.v074.i02> for further details on estimation and the package structure. For tutorials on how to use the CDM package see George and Robitzsch (2015) as well as Ravand and Robitzsch (2015).
Author: Alexander Robitzsch [aut, cre], Thomas Kiefer [aut], Ann Cathrice George [aut], Ali Uenlue [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package ICRanks updated to version 2.0 with previous version 1.3 dated 2017-11-21

Title: Simultaneous Confidence Intervals for Ranks
Description: Algorithms to construct simultaneous confidence intervals for the ranks of means mu_1,...,mu_n based on an independent Gaussian sample using multiple testing techniques.
Author: Diaa Al Mohamad and Erik W. van Zwet and Jelle J. Goeman
Maintainer: Diaa Al Mohamad <diaa.almohamad@gmail.com>

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Package fingertipscharts updated to version 0.0.3 with previous version 0.0.2 dated 2018-09-14

Title: Produce Charts that you See on the Fingertips Website
Description: Use Fingertips charts to recreate the visualisations that are displayed on the Fingertips website (<http://fingertips.phe.org.uk/>).
Author: Sebastian Fox [aut, cre]
Maintainer: Sebastian Fox <sebastian.fox@phe.gov.uk>

Diff between fingertipscharts versions 0.0.2 dated 2018-09-14 and 0.0.3 dated 2018-12-13

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Package crypto updated to version 1.1.0 with previous version 1.0.3 dated 2018-09-20

Title: Crypto Currency Market Data
Description: Retrieves crypto currency current and historical information as well as information on the exchanges they are listed on. For current and historical it will retrieve the daily open, high, low and close values for all crypto currencies. This retrieves the historical market data by web scraping tables provided by 'Cryptocurrency Market Capitalizations' <https://coinmarketcap.com>.
Author: Jesse Vent [aut, cre]
Maintainer: Jesse Vent <cryptopackage@icloud.com>

Diff between crypto versions 1.0.3 dated 2018-09-20 and 1.1.0 dated 2018-12-13

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Package MESS updated to version 0.5.4 with previous version 0.5.3 dated 2018-11-23

Title: Miscellaneous Esoteric Statistical Scripts
Description: A mixed collection of useful and semi-useful diverse statistical functions, some of which may even be referenced in The R Primer book.
Author: Claus Thorn Ekstrøm [aut, cre]
Maintainer: Claus Thorn Ekstrøm <claus@rprimer.dk>

Diff between MESS versions 0.5.3 dated 2018-11-23 and 0.5.4 dated 2018-12-13

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Package libcoin updated to version 1.0-2 with previous version 1.0-1 dated 2017-12-13

Title: Linear Test Statistics for Permutation Inference
Description: Basic infrastructure for linear test statistics and permutation inference in the framework of Strasser and Weber (1999) <http://epub.wu.ac.at/102/>. This package must not be used by end-users. CRAN package 'coin' implements all user interfaces and is ready to be used by anyone.
Author: Torsten Hothorn [aut, cre]
Maintainer: Torsten Hothorn <Torsten.Hothorn@R-project.org>

Diff between libcoin versions 1.0-1 dated 2017-12-13 and 1.0-2 dated 2018-12-13

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Package StanHeaders updated to version 2.18.0-1 with previous version 2.18.0 dated 2018-10-07

Title: C++ Header Files for Stan
Description: The C++ header files of the Stan project are provided by this package, but it contains no R code or function documentation. There is a shared object containing part of the 'CVODES' library, but it is not accessible from R. 'StanHeaders' is only useful for developers who want to utilize the 'LinkingTo' directive of their package's DESCRIPTION file to build on the Stan library without incurring unnecessary dependencies. The Stan project develops a probabilistic programming language that implements full or approximate Bayesian statistical inference via Markov Chain Monte Carlo or 'variational' methods and implements (optionally penalized) maximum likelihood estimation via optimization. The Stan library includes an advanced automatic differentiation scheme, 'templated' statistical and linear algebra functions that can handle the automatically 'differentiable' scalar types (and doubles, 'ints', etc.), and a parser for the Stan language. The 'rstan' package provides user-facing R functions to parse, compile, test, estimate, and analyze Stan models.
Author: Ben Goodrich [cre, aut], Joshua Pritikin [ctb], Andrew Gelman [aut], Bob Carpenter [aut], Matt Hoffman [aut], Daniel Lee [aut], Michael Betancourt [aut], Marcus Brubaker [aut], Jiqiang Guo [aut], Peter Li [aut], Allen Riddell [aut], Marco Inacio [aut], Mitzi Morris [aut], Jeffrey Arnold [aut], Rob Goedman [aut], Brian Lau [aut], Rob Trangucci [aut], Jonah Gabry [aut], Alp Kucukelbir [aut], Robert Grant [aut], Dustin Tran [aut], Michael Malecki [aut], Yuanjun Gao [aut], Trustees of Columbia University [cph], Lawrence Livermore National Security [cph] (CVODES), The Regents of the University of California [cph] (CVODES), Southern Methodist University [cph] (CVODES)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>

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Package harrypotter updated to version 2.0.0 with previous version 0.1.0 dated 2018-09-03

Title: Palettes Generated from All "Harry Potter" Movies
Description: Implementation of the characteristic palette of the houses of Hogwarts School of magic, present in all Harry Potter movies.
Author: Alejandro Jimenez Rico [aut, cre]
Maintainer: Alejandro Jimenez Rico <aljrico@gmail.com>

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Package solrium updated to version 1.0.2 with previous version 1.0.0 dated 2017-11-02

Title: General Purpose R Interface to 'Solr'
Description: Provides a set of functions for querying and parsing data from 'Solr' (<http://lucene.apache.org/solr>) 'endpoints' (local and remote), including search, 'faceting', 'highlighting', 'stats', and 'more like this'. In addition, some functionality is included for creating, deleting, and updating documents in a 'Solr' 'database'.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>

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Package rwalkr updated to version 0.4.0 with previous version 0.3.4 dated 2018-07-19

Title: API to Melbourne Pedestrian Data
Description: Provides API to Melbourne pedestrian data in tidy data form.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>)
Maintainer: Earo Wang <earo.wang@gmail.com>

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Wed, 12 Dec 2018

Package MachineShop updated to version 0.4.0 with previous version 0.3.0 dated 2018-11-23

Title: Machine Learning Models and Tools
Description: Meta-package for statistical and machine learning with a common interface for model fitting, prediction, performance assessment, and presentation of results. Supports predictive modeling of numerical, categorical, and censored time-to-event outcomes and resample (bootstrap and cross-validation) estimation of model performance.
Author: Brian J Smith [aut, cre]
Maintainer: Brian J Smith <brian-j-smith@uiowa.edu>

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Package jstor updated to version 0.3.6 with previous version 0.3.5 dated 2018-11-25

Title: Read Data from JSTOR/DfR
Description: Functions and helpers to import metadata, ngrams and full-texts delivered by Data for Research by JSTOR.
Author: Thomas Klebel [aut, cre] (<https://orcid.org/0000-0002-7331-4751>)
Maintainer: Thomas Klebel <t.klebel@hotmail.com>

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Package jsr223 updated to version 0.3.3 with previous version 0.3.2 dated 2018-04-30

Title: A 'Java' Platform Integration for 'R' with Programming Languages 'Groovy', 'JavaScript', 'JRuby' ('Ruby'), 'Jython' ('Python'), and 'Kotlin'
Description: Provides a high-level integration for the 'Java' platform that makes 'Java' objects easy to use from within 'R'; provides a unified interface to integrate 'R' with several programming languages; and features extensive data exchange between 'R' and 'Java'. The 'jsr223'-supported programming languages include 'Groovy', 'JavaScript', 'JRuby' ('Ruby'), 'Jython' ('Python'), and 'Kotlin'. Any of these languages can use and extend 'Java' classes in natural syntax. Furthermore, solutions developed in any of the 'jsr223'-supported languages are also accessible to 'R' developers. The 'jsr223' package also features callbacks, script compiling, and string interpolation. In all, 'jsr223' significantly extends the computing capabilities of the 'R' software environment.
Author: Floid R. Gilbert [aut, cre], David B. Dahl [aut]
Maintainer: Floid R. Gilbert <floid.r.gilbert@gmail.com>

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Package healthcareai updated to version 2.3.0 with previous version 2.2.0 dated 2018-09-01

Title: Tools for Healthcare Machine Learning
Description: A machine learning toolbox tailored to healthcare data.
Author: Levi Thatcher [aut], Michael Levy [aut], Mike Mastanduno [aut, cre], Taylor Larsen [aut], Taylor Miller [aut], Rex Sumsion [aut]
Maintainer: Mike Mastanduno <michael.mastanduno@healthcatalyst.com>

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Package SMFilter updated to version 1.0.3 with previous version 1.0.2 dated 2018-12-03

Title: Filtering Algorithms for the State Space Models on the Stiefel Manifold
Description: Provides the filtering algorithms for the state space models on the Stiefel manifold as well as the corresponding sampling algorithms for uniform, vector Langevin-Bingham and matrix Langevin-Bingham distributions on the Stiefel manifold.
Author: Yukai Yang [aut, cre]
Maintainer: Yukai Yang <yukai.yang@statistik.uu.se>

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Package parallelDist updated to version 0.2.4 with previous version 0.2.3 dated 2018-12-11

Title: Parallel Distance Matrix Computation using Multiple Threads
Description: A fast parallelized alternative to R's native 'dist' function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices, which supports a broad variety of 41 predefined distance functions from the 'stats', 'proxy' and 'dtw' R packages, as well as user- defined functions written in C++. For ease of use, the 'parDist' function extends the signature of the 'dist' function and uses the same parameter naming conventions as distance methods of existing R packages. The package is mainly implemented in C++ and leverages the 'RcppParallel' package to parallelize the distance computations with the help of the 'TinyThread' library. Furthermore, the 'Armadillo' linear algebra library is used for optimized matrix operations during distance calculations. The curiously recurring template pattern (CRTP) technique is applied to avoid virtual functions, which improves the Dynamic Time Warping calculations while the implementation stays flexible enough to support different DTW step patterns and normalization methods.
Author: Alexander Eckert [aut, cre], Lucas Godoy [ctb], Srikanth KS [ctb]
Maintainer: Alexander Eckert <info@alexandereckert.com>

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Package distances updated to version 0.1.6 with previous version 0.1.5 dated 2018-12-12

Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

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Package tractor.base updated to version 3.3.0 with previous version 3.2.2 dated 2018-03-16

Title: Read, Manipulate and Visualise Magnetic Resonance Images
Description: Functions for working with magnetic resonance images. Reading and writing of popular file formats (DICOM, Analyze, NIfTI-1, NIfTI-2, MGH); interactive and non-interactive visualisation; flexible image manipulation; metadata and sparse image handling.
Author: Jon Clayden
Maintainer: Jon Clayden <code@clayden.org>

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Package basicMCMCplots updated to version 0.1.2 with previous version 0.1.1 dated 2018-11-29

Title: Trace Plots, Density Plots and Chain Comparisons for MCMC Samples
Description: Provides a function for examining posterior MCMC samples from a single chain using trace plots and density plots, and from multiple chains by comparing posterior medians and credible intervals from each chain. These plotting functions have a variety of options, such as figure sizes, legends, parameters to plot, and saving plots to file. Functions interface with the NIMBLE software package, see de Valpine, Turek, Paciorek, Anderson-Bergman, Temple Lang and Bodik (2017) <doi:10.1080/10618600.2016.1172487>.
Author: Daniel Turek [aut, cre]
Maintainer: Daniel Turek <danielturek@gmail.com>

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Package STARTS updated to version 1.0-6 with previous version 0.5-28 dated 2018-11-12

Title: Functions for the STARTS Model
Description: Contains functions for estimating the STARTS model of Kenny and Zautra (1995, 2001) <DOI:10.1037/0022-006X.63.1.52>, <DOI:10.1037/10409-008>. Penalized maximum likelihood estimation and Markov Chain Monte Carlo estimation are also provided, see Luedtke, Robitzsch and Wagner (2018) <DOI:10.1037/met0000155>.
Author: Alexander Robitzsch [aut,cre], Oliver Luedtke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package bamp updated to version 2.0.5 with previous version 2.0.4 dated 2018-11-30

Title: Bayesian Age-Period-Cohort Modeling and Prediction
Description: Bayesian Age-Period-Cohort Modeling and Prediction using efficient Markov Chain Monte Carlo Methods. This is the R version of the previous BAMP software as described in Volker Schmid and Leonhard Held (2007) <DOI:10.18637/jss.v021.i08> Bayesian Age-Period-Cohort Modeling and Prediction - BAMP, Journal of Statistical Software 21:8. This package includes checks of convergence using Gelman's R.
Author: Volker Schmid [aut, cre], Florian Geressen [ctb], Leonhard Held [ctb], Evi Rainer [ctb]
Maintainer: Volker Schmid <volker.schmid@lmu.de>

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Package mvbutils updated to version 2.8.232 with previous version 2.7.4.1 dated 2013-04-17

Title: Workspace Organization, Code and Documentation Editing, Package Prep and Editing, Etc
Description: Hierarchical workspace tree, code editing and backup, easy package prep, editing of packages while loaded, per-object lazy-loading, easy documentation, macro functions, and miscellaneous utilities. Needed by debug package.
Author: Mark V. Bravington <mark.bravington@csiro.au>
Maintainer: Mark V. Bravington <mark.bravington@csiro.au>

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Package metaboGSE updated to version 1.2.1 with previous version 1.2.0 dated 2018-11-22

Title: Gene Set Enrichment Analysis via Integration of Metabolic Networks and RNA-Seq Data
Description: Integrates metabolic networks and RNA-seq data to construct condition-specific series of metabolic sub-networks and applies to gene set enrichment analysis (Tran et al. (2018) <doi:10.1093/bioinformatics/bty929>).
Author: Van Du T. Tran [aut, cre], Marco Pagni [aut]
Maintainer: Van Du T. Tran <thuong.tran@sib.swiss>

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Package glmc updated to version 0.3-1 with previous version 0.2-4 dated 2012-12-04

Title: Fitting Generalized Linear Models Subject to Constraints
Description: Fits generalized linear models where the parameters are subject to linear constraints. The model is specified by giving a symbolic description of the linear predictor, a description of the error distribution, and a matrix of constraints on the parameters.
Author: Sanjay Chaudhuri [aut, cre], Mark S. Handcock [aut], Michael S. Rendall [ctb]
Maintainer: Sanjay Chaudhuri <sanjay@stat.nus.edu.sg>

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Package binneR updated to version 2.0.5 with previous version 1.1.1 dated 2018-03-01

Title: Spectral Processing for High Resolution Flow Infusion Mass Spectrometry
Description: A spectral binning approach for high resolution flow infusion mass spectrometry data.
Author: Jasen Finch [aut, cre]
Maintainer: Jasen Finch <jsf9@aber.ac.uk>

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Package skynet updated to version 1.3.0 with previous version 1.2.2 dated 2018-06-28

Title: Generates Networks from BTS Data
Description: A flexible tool that allows generating bespoke air transport statistics for urban studies based on publicly available data from the Bureau of Transport Statistics (BTS) in the United States <https://www.transtats.bts.gov/databases.asp?Mode_ID=1&Mode_Desc=Aviation&Subject_ID2=0>.
Author: Filipe Teixeira [aut, cre]
Maintainer: Filipe Teixeira <Filipe.MarquesTeixeira@Ugent.be>

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Package xtensor updated to version 0.9.0-0 with previous version 0.8.1-0 dated 2018-10-19

Title: Headers for the 'xtensor' Library
Description: The 'xtensor' C++ library for numerical analysis with multi-dimensional array expressions is provided as a header-only C++14 library. It offers an extensible expression system enabling lazy broadcasting; an API following the idioms of the C++ standard library; and tools to manipulate array expressions and build upon 'xtensor'.
Author: Johan Mabille, Sylvain Corlay and Wolf Vollprecht
Maintainer: Sylvain Corlay <sylvain.corlay@gmail.com>

Diff between xtensor versions 0.8.1-0 dated 2018-10-19 and 0.9.0-0 dated 2018-12-12

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Package tsibble updated to version 0.6.2 with previous version 0.6.1 dated 2018-12-05

Title: Tidy Temporal Data Frames and Tools
Description: Provides a 'tbl_ts' class (the 'tsibble') to store and manage temporal data in a data-centric format, which is built on top of the 'tibble'. The 'tsibble' aims at easily manipulating and analysing temporal data, including counting and filling time gaps, aggregate over calendar periods, performing rolling window calculations, and etc.
Author: Earo Wang [aut, cre] (<https://orcid.org/0000-0001-6448-5260>), Di Cook [aut, ths] (<https://orcid.org/0000-0002-3813-7155>), Rob Hyndman [aut, ths] (<https://orcid.org/0000-0002-2140-5352>), Mitchell O'Hara-Wild [ctb]
Maintainer: Earo Wang <earo.wang@gmail.com>

Diff between tsibble versions 0.6.1 dated 2018-12-05 and 0.6.2 dated 2018-12-12

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Package NetworkDistance updated to version 0.3.1 with previous version 0.3.0 dated 2018-10-05

Title: Distance Measures for Networks
Description: Network is a prevalent form of data structure in many fields. As an object of analysis, many distance or metric measures have been proposed to define the concept of similarity between two networks. We provide a number of distance measures for networks. See Jurman et al (2011) <doi:10.3233/978-1-60750-692-8-227> for an overview on spectral class of inter-graph distance measures.
Author: Kisung You [aut, cre] (<https://orcid.org/0000-0002-8584-459X>)
Maintainer: Kisung You <kyou@nd.edu>

Diff between NetworkDistance versions 0.3.0 dated 2018-10-05 and 0.3.1 dated 2018-12-12

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Package distances updated to version 0.1.5 with previous version 0.1.4 dated 2018-08-15

Title: Tools for Distance Metrics
Description: Provides tools for constructing, manipulating and using distance metrics.
Author: Fredrik Savje [aut, cre]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between distances versions 0.1.4 dated 2018-08-15 and 0.1.5 dated 2018-12-12

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Package exprso updated to version 0.4.7 with previous version 0.4.0 dated 2018-07-25

Title: Rapid Deployment of Machine Learning Algorithms
Description: Supervised machine learning has an increasingly important role in data analysis. This package introduces a framework for rapidly building and deploying supervised machine learning in a high-throughput manner. This package provides a user-friendly interface that empowers investigators to execute state-of-the-art binary and multi-class classification, as well as regression, with minimal programming experience necessary.
Author: Thomas Quinn [aut, cre], Daniel Tylee [ctb], Samuel Lee [ctb]
Maintainer: Thomas Quinn <contacttomquinn@gmail.com>

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Package scclust updated to version 0.2.1 with previous version 0.2.0 dated 2018-08-24

Title: Size-Constrained Clustering
Description: Provides wrappers for 'scclust', a C library for computationally efficient size-constrained clustering with near-optimal performance. See <https://github.com/fsavje/scclust> for more information.
Author: Fredrik Savje [aut, cre], Michael Higgins [aut], Jasjeet Sekhon [aut]
Maintainer: Fredrik Savje <fredrik.savje@yale.edu>

Diff between scclust versions 0.2.0 dated 2018-08-24 and 0.2.1 dated 2018-12-12

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Tue, 11 Dec 2018

Package rsMove updated to version 0.2.7 with previous version 0.2.6 dated 2018-10-24

Title: Guidelines for the use of Remote Sensing in Movement Ecology
Description: Tools for the guided selection of satellite data and environmental predictors, the combination of remote sensing and animal movement data and the mapping of resource suitabilitz. Based on the paper by Remelgado et al. (2015) <doi:10.1002/rse2.70>.
Author: Ruben Remelgado [aut, cre]
Maintainer: Ruben Remelgado <remelgado.ruben@gmail.com>

Diff between rsMove versions 0.2.6 dated 2018-10-24 and 0.2.7 dated 2018-12-11

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Package RcppParallel updated to version 4.4.2 with previous version 4.4.1 dated 2018-07-19

Title: Parallel Programming Tools for 'Rcpp'
Description: High level functions for parallel programming with 'Rcpp'. For example, the 'parallelFor()' function can be used to convert the work of a standard serial "for" loop into a parallel one and the 'parallelReduce()' function can be used for accumulating aggregate or other values.
Author: JJ Allaire [aut], Romain Francois [aut, cph], Kevin Ushey [aut, cre], Gregory Vandenbrouck [aut], Marcus Geelnard [aut, cph] (TinyThread library, http://tinythreadpp.bitsnbites.eu/), RStudio [cph], Intel [aut, cph] (Intel TBB library, https://www.threadingbuildingblocks.org/), Microsoft [cph]
Maintainer: Kevin Ushey <kevin@rstudio.com>

Diff between RcppParallel versions 4.4.1 dated 2018-07-19 and 4.4.2 dated 2018-12-11

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Package parallelDist updated to version 0.2.3 with previous version 0.2.2 dated 2018-09-24

Title: Parallel Distance Matrix Computation using Multiple Threads
Description: A fast parallelized alternative to R's native 'dist' function to calculate distance matrices for continuous, binary, and multi-dimensional input matrices, which supports a broad variety of 41 predefined distance functions from the 'stats', 'proxy' and 'dtw' R packages, as well as user- defined functions written in C++. For ease of use, the 'parDist' function extends the signature of the 'dist' function and uses the same parameter naming conventions as distance methods of existing R packages. The package is mainly implemented in C++ and leverages the 'RcppParallel' package to parallelize the distance computations with the help of the 'TinyThread' library. Furthermore, the 'Armadillo' linear algebra library is used for optimized matrix operations during distance calculations. The curiously recurring template pattern (CRTP) technique is applied to avoid virtual functions, which improves the Dynamic Time Warping calculations while the implementation stays flexible enough to support different DTW step patterns and normalization methods.
Author: Alexander Eckert [aut, cre], Lucas Godoy [ctb], Srikanth KS [ctb]
Maintainer: Alexander Eckert <info@alexandereckert.com>

Diff between parallelDist versions 0.2.2 dated 2018-09-24 and 0.2.3 dated 2018-12-11

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Package glmm updated to version 1.3.0 with previous version 1.2.3 dated 2018-02-22

Title: Generalized Linear Mixed Models via Monte Carlo Likelihood Approximation
Description: Approximates the likelihood of a generalized linear mixed model using Monte Carlo likelihood approximation. Then maximizes the likelihood approximation to return maximum likelihood estimates, observed Fisher information, and other model information.
Author: Christina Knudson [aut, cre], Charles J. Geyer [ctb], Sydney Benson [ctb]
Maintainer: Christina Knudson <knud8583@stthomas.edu>

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Package fieldRS updated to version 0.2.1 with previous version 0.1.1 dated 2018-09-16

Title: Remote Sensing Field Work Tools
Description: In remote sensing, designing a field campaign to collect ground-truth data can be a challenging task. We need to collect representative samples while accounting for issues such as budget constraints and limited accessibility created by e.g. poor infrastructure. As suggested by Olofsson et al. (2014) <doi:10.1016/j.rse.2014.02.015>, this demands the establishment of best-practices to collect ground-truth data that avoid the waste of time and funds. 'fieldRS' addresses this issue by helping scientists and practitioners design field campaigns through the identification of priority sampling sites, the extraction of potential sampling plots and the conversion of plots into consistent training and validation samples that can be used in e.g. land cover classification.
Author: Ruben Remelgado [aut, cre]
Maintainer: Ruben Remelgado <remelgado.ruben@gmail.com>

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Package CsChange updated to version 0.1.5 with previous version 0.1.4 dated 2018-06-13

Title: Testing for Change in C-Statistic
Description: Calculate the confidence interval and p value for change in C-statistic. The adjusted C-statistic is calculated by using formula as "Somers' Dxy rank correlation"/2+0.5. The confidence interval was calculated by using the bootstrap method. The p value was calculated by using the Z testing method. Please refer to the article of Peter Ganz et al. (2016) <doi:10.1001/jama.2016.5951>.
Author: Zhicheng Du, Yuantao Hao
Maintainer: Zhicheng Du<dgdzc@hotmail.com>

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Package rbi updated to version 0.10.0 with previous version 0.9.1 dated 2018-05-14

Title: R Interface to LibBi
Description: Provides a complete R interface to LibBi, a library for Bayesian inference (see <http://libbi.org> and <doi:10.18637/jss.v067.i10> for more information). This includes functions for manipulating LibBi models, for reading and writing LibBi input/output files, for converting LibBi output to provide traces for use with the coda package, and for running LibBi from R.
Author: Pierre E. Jacob [aut], Anthony Lee [ctb], Lawrence M. Murray [ctb], Sebastian Funk [aut, cre], Sam Abbott [ctb]
Maintainer: Sebastian Funk <sebastian.funk@lshtm.ac.uk>

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Package MVar.pt updated to version 2.0.3 with previous version 2.0.2 dated 2018-06-13

Title: Analise multivariada (brazilian portuguese)
Description: Pacote para analise multivariada, tendo funcoes que executam analise de correspondencia simples (CA) e multipla (MCA), analise de componentes principais (PCA), analise de correlacao canonica (CCA), analise fatorial (FA), escalonamento multidimensional (MDS), analise de cluster hierarquico e nao hierarquico, regressao linear, analise de multiplos fatores (MFA) para dados quantitativos, qualitativos, de frequencia (MFACT) e dados mistos, projection pursuit (PP), grant tour e outras funcoes uteis para a analise multivariada.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Package diagmeta updated to version 0.3-0 with previous version 0.2-0 dated 2018-03-23

Title: Meta-Analysis of Diagnostic Accuracy Studies with Several Cutpoints
Description: Provides methods by Steinhauser et al. (2016) <DOI:10.1186/s12874-016-0196-1> for meta-analysis of diagnostic accuracy studies with several cutpoints.
Author: Gerta Rücker [aut], Susanne Steinhauser [aut], Srinath Kolampally [aut], Guido Schwarzer [aut, cre]
Maintainer: Guido Schwarzer <sc@imbi.uni-freiburg.de>

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Package MVar updated to version 2.0.3 with previous version 2.0.2 dated 2018-06-15

Title: Multivariate Analysis
Description: Package for multivariate analysis, having functions that perform simple correspondence analysis (CA) and multiple correspondence analysis (MCA), principal components analysis (PCA), canonical correlation analysis (CCA), factorial analysis (FA), multidimensional scaling (MDS), hierarchical and non-hierarchical cluster analysis, linear regression, multiple factor analysis (MFA) for quantitative, qualitative, frequency (MFACT) and mixed data, projection pursuit (PP), grant tour method and other useful functions for the multivariate analysis.
Author: Paulo Cesar Ossani <ossanipc@hotmail.com> Marcelo Angelo Cirillo <macufla@des.ufla.br>
Maintainer: Paulo Cesar Ossani <ossanipc@hotmail.com>

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Package osqp updated to version 0.5.0 with previous version 0.4.1 dated 2018-09-27

Title: Quadratic Programming Solver using the 'OSQP' Library
Description: Provides bindings to the 'OSQP' solver. The 'OSQP' solver is a numerical optimization package or solving convex quadratic programs written in 'C' and based on the alternating direction method of multipliers, 'ADMM'. B. Stellato, G. Banjac, P. Goulart, A. Bemporad, S. Boyd (2018) <arXiv:1711.08013>.
Author: Bartolomeo Stellato [cre, aut, ctb, cph], Goran Banjac [aut, ctb, cph], Paul Goulart [aut, ctb, cph], Stephen Boyd [aut, ctb, cph], Eric Anderson [ctb]
Maintainer: Bartolomeo Stellato <bartolomeo.stellato@gmail.com>

Diff between osqp versions 0.4.1 dated 2018-09-27 and 0.5.0 dated 2018-12-11

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Package ivtools updated to version 2.1.0 with previous version 2.0.0 dated 2018-11-05

Title: Instrumental Variables
Description: Contains tools for instrumental variables estimation. Currently, non-parametric bounds, two-stage estimation and G-estimation are implemented. Balke, A. and Pearl, J. (1997) <doi:10.2307/2965583>, Vansteelandt S., Bowden J., Babanezhad M., Goetghebeur E. (2011) <doi:10.1214/11-STS360>.
Author: Arvid Sjolander, Elisabeth Dahlqwist, Torben Martinussen
Maintainer: Arvid Sjolander <arvid.sjolander@ki.se>

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Package pdftools updated to version 2.0 with previous version 1.8 dated 2018-05-27

Title: Text Extraction, Rendering and Converting of PDF Documents
Description: Utilities based on 'libpoppler' for extracting text, fonts, attachments and metadata from a PDF file. Also supports high quality rendering of PDF documents info PNG, JPEG, TIFF format, or into raw bitmap vectors for further processing in R.
Author: Jeroen Ooms [aut, cre] (<https://orcid.org/0000-0002-4035-0289>)
Maintainer: Jeroen Ooms <jeroen@berkeley.edu>

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Package HCmodelSets updated to version 1.0.0 with previous version 0.2.1 dated 2018-11-27

Title: Regression with a Large Number of Potential Explanatory Variables
Description: Software for performing the reduction, exploratory and model selection phases of the procedure proposed by Cox, D.R. and Battey, H.S. (2017) <doi:10.1073/pnas.1703764114> for sparse regression when the number of potential explanatory variables far exceeds the sample size. The software supports linear regression, likelihood-based fitting of generalized linear regression models and the proportional hazards model fitted by partial likelihood.
Author: H. H. Hoeltgebaum
Maintainer: H. H. Hoeltgebaum <hh3015@ic.ac.uk>

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Package expss updated to version 0.8.10 with previous version 0.8.8 dated 2018-11-11

Title: Tables with Labels and Some Useful Functions from Spreadsheets and 'SPSS' Statistics
Description: Package provides tabulation functions with support for 'SPSS'-style labels, multiple / nested banners, weights, multiple-response variables and significance testing. There are facilities for nice output of tables in 'knitr', 'Shiny', R and 'Jupyter' notebooks, '*.xlsx' files. Proper methods for labelled variables add value labels support to base R functions and to some functions from other packages. Additionally, the package offers useful functions for data processing in marketing research / social surveys - popular data transformation functions from 'SPSS' Statistics ('RECODE', 'COUNT', 'COMPUTE', 'DO IF', etc.) and 'Excel' ('COUNTIF', 'VLOOKUP', etc.). Package is intended to help people to move data processing from 'Excel'/'SPSS' to R.
Author: Gregory Demin [aut, cre]
Maintainer: Gregory Demin <gdemin@gmail.com>

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Package MoEClust updated to version 1.2.1 with previous version 1.2.0 dated 2018-08-24

Title: Gaussian Parsimonious Clustering Models with Covariates
Description: Clustering via parsimonious Gaussian Mixtures of Experts using the MoEClust models introduced by Murphy and Murphy (2017) <arXiv:1711.05632>. This package fits finite Gaussian mixture models with a formula interface for supplying gating and/or expert network covariates using a range of parsimonious covariance parameterisations via the EM/CEM algorithm. Visualisation of the results of such models using generalised pairs plots is also facilitated.
Author: Keefe Murphy [aut, cre], Thomas Brendan Murphy [ctb]
Maintainer: Keefe Murphy <keefe.murphy@ucd.ie>

Diff between MoEClust versions 1.2.0 dated 2018-08-24 and 1.2.1 dated 2018-12-11

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Package miceadds updated to version 3.0-16 with previous version 2.15-22 dated 2018-10-19

Title: Some Additional Multiple Imputation Functions, Especially for 'mice'
Description: Contains functions for multiple imputation which complements existing functionality in R. In particular, several imputation methods for the mice package (van Buuren & Groothuis-Oudshoorn, 2011, <doi:10.18637/jss.v045.i03>) are included. Main features of the miceadds package include plausible value imputation (Mislevy, 1991, <doi:10.1007/BF02294457>), multilevel imputation for variables at any level or with any number of hierarchical and non-hierarchical levels (Grund, Luedtke & Robitzsch, 2018, <doi:10.1177/1094428117703686>; van Buuren, 2018, Ch.7, <doi:10.1201/9780429492259>), imputation using partial least squares (PLS) for high dimensional predictors (Robitzsch, Pham & Yanagida, 2016), and nested multiple imputation (Rubin, 2003, <doi:10.1111/1467-9574.00217>).
Author: Alexander Robitzsch [aut, cre], Simon Grund [aut], Thorsten Henke [aut]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

Diff between miceadds versions 2.15-22 dated 2018-10-19 and 3.0-16 dated 2018-12-11

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Package BIFIEsurvey updated to version 3.0-14 with previous version 2.191-12 dated 2018-10-17

Title: Tools for Survey Statistics in Educational Assessment
Description: Contains tools for survey statistics (especially in educational assessment) for datasets with replication designs (jackknife, bootstrap, replicate weights; see Kolenikov, 2010; Pfefferman & Rao, 2009a, 2009b, <doi:10.1016/S0169-7161(09)70003-3>, <doi:10.1016/S0169-7161(09)70037-9>); Shao, 1996, <doi:10.1080/02331889708802523>). Descriptive statistics, linear and logistic regression, path models for manifest variables with measurement error correction and two-level hierarchical regressions for weighted samples are included. Statistical inference can be conducted for multiply imputed datasets and nested multiply imputed datasets and is in particularly suited for the analysis of plausible values (for details see George, Oberwimmer & Itzlinger-Bruneforth, 2016; Bruneforth, Oberwimmer & Robitzsch, 2016; Robitzsch, Pham & Yanagida, 2016; <doi:10.17888/fdb-demo:bistE813I-16a>). This package is developed by BIFIE (Federal Institute for Educational Research, Innovation and Development of the Austrian School System; Salzburg, Austria).
Author: BIFIE [aut], Alexander Robitzsch [ctb, cre], Konrad Oberwimmer [ctb]
Maintainer: Alexander Robitzsch <robitzsch@ipn.uni-kiel.de>

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Package extremefit updated to version 0.2.5 with previous version 0.2.4 dated 2018-11-28

Title: Estimation of Extreme Conditional Quantiles and Probabilities
Description: Extreme value theory, nonparametric kernel estimation, tail conditional probabilities, extreme conditional quantile, adaptive estimation, quantile regression, survival probabilities.
Author: Gilles Durrieu, Ion Grama, Kevin Jaunatre, Quang-Khoai Pham, Jean-Marie Tricot
Maintainer: Kevin Jaunatre <kevin.jaunatre@univ-ubs.fr>

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Package ANN2 updated to version 2.0 with previous version 1.5 dated 2017-11-28

Title: Artificial Neural Networks for Anomaly Detection
Description: Training of neural networks for classification and regression tasks using mini-batch gradient descent. Special features include a function for training autoencoders, which can be used to detect anomalies, and some related plotting functions. Multiple activation functions are supported, including tanh, relu, step and ramp. For the use of the step and ramp activation functions in detecting anomalies using autoencoders, see Hawkins et al. (2002) <doi:10.1007/3-540-46145-0_17>. Furthermore, several loss functions are supported, including robust ones such as Huber and pseudo-Huber loss, as well as L1 and L2 regularization. The possible options for optimization algorithms are RMSprop, Adam and SGD with momentum. The package contains a vectorized C++ implementation that facilitates fast training through mini-batch learning.
Author: Bart Lammers
Maintainer: Bart Lammers <bart.f.lammers@gmail.com>

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Package readr updated to version 1.3.0 with previous version 1.2.0 dated 2018-11-22

Title: Read Rectangular Text Data
Description: The goal of 'readr' is to provide a fast and friendly way to read rectangular data (like 'csv', 'tsv', and 'fwf'). It is designed to flexibly parse many types of data found in the wild, while still cleanly failing when data unexpectedly changes.
Author: Hadley Wickham [aut], Jim Hester [aut, cre], Romain Francois [aut], R Core Team [ctb] (Date time code adapted from R), RStudio [cph, fnd], Jukka Jylänki [ctb, cph] (grisu3 implementation), Mikkel Jørgensen [ctb, cph] (grisu3 implementation)
Maintainer: Jim Hester <james.hester@rstudio.com>

Diff between readr versions 1.2.0 dated 2018-11-22 and 1.3.0 dated 2018-12-11

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Package pbdDMAT updated to version 0.5-0 with previous version 0.4-2 dated 2016-10-21

Title: 'pbdR' Distributed Matrix Methods
Description: A set of classes for managing distributed matrices, and a collection of methods for computing linear algebra and statistics. Computation is handled mostly by routines from the 'pbdBASE' package, which itself relies on the 'ScaLAPACK' and 'PBLAS' numerical libraries for distributed computing.
Author: Drew Schmidt [aut, cre], Wei-Chen Chen [aut], Sebastien Lamy de la Chapelle [aut], George Ostrouchov [aut], Pragneshkumar Patel [aut], ZhaoKang Wang [ctb], Michael Lawrence [ctb], R Core team [ctb] (some wrappers taken from the base and stats packages)
Maintainer: Drew Schmidt <wrathematics@gmail.com>

Diff between pbdDMAT versions 0.4-2 dated 2016-10-21 and 0.5-0 dated 2018-12-11

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More information about pbdDMAT at CRAN
Permanent link

Package lpirfs updated to version 0.1.4 with previous version 0.1.3 dated 2018-09-29

Title: Local Projections Impulse Response Functions
Description: Provides functions to estimate and plot linear as well as nonlinear impulse responses based on local projections by Jordà (2005) <doi:10.1257/0002828053828518>.
Author: Philipp Adämmer [aut, cre] (<https://orcid.org/0000-0003-3770-0097>), James P. LeSage [ctb], Mehmet Balcilar [ctb]
Maintainer: Philipp Adämmer <adaemmer@hsu-hh.de>

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More information about lpirfs at CRAN
Permanent link

Package geogrid updated to version 0.1.1 with previous version 0.1.0.1 dated 2018-08-19

Title: Turn Geospatial Polygons into Regular or Hexagonal Grids
Description: Turn irregular polygons (such as geographical regions) into regular or hexagonal grids. This package enables the generation of regular (square) and hexagonal grids through the package 'sp' and then assigns the content of the existing polygons to the new grid using the Hungarian algorithm, Kuhn (1955) (<doi:10.1007/978-3-540-68279-0_2>). This prevents the need for manual generation of hexagonal grids or regular grids that are supposed to reflect existing geography.
Author: Joseph Bailey [aut, cre], Ryan Hafen [ctb], Jakub Nowosad [ctb] (<https://orcid.org/0000-0002-1057-3721>), Lars Simon Zehnder [ctb] (RcppArmadillo implmentation of Munkres' Assignment Algorithm)
Maintainer: Joseph Bailey <jbailey@futurecities.catapult.org.uk>

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More information about geogrid at CRAN
Permanent link

Package animation updated to version 2.6 with previous version 2.5 dated 2017-03-30

Title: A Gallery of Animations in Statistics and Utilities to Create Animations
Description: Provides functions for animations in statistics, covering topics in probability theory, mathematical statistics, multivariate statistics, non-parametric statistics, sampling survey, linear models, time series, computational statistics, data mining and machine learning. These functions may be helpful in teaching statistics and data analysis. Also provided in this package are a series of functions to save animations to various formats, e.g. Flash, 'GIF', HTML pages, 'PDF' and videos. 'PDF' animations can be inserted into 'Sweave' / 'knitr' easily.
Author: Yihui Xie [aut, cre], Christian Mueller [ctb], Lijia Yu [ctb], Weicheng Zhu [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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More information about animation at CRAN
Permanent link

Package smoothr updated to version 0.1.1 with previous version 0.1.0 dated 2018-04-04

Title: Smooth and Tidy Spatial Features
Description: Tools for smoothing and tidying spatial features (i.e. lines and polygons) to make them more aesthetically pleasing. Smooth curves, fill holes, and remove small fragments from lines and polygons.
Author: Matthew Strimas-Mackey [aut, cre] (<https://orcid.org/0000-0001-8929-7776>)
Maintainer: Matthew Strimas-Mackey <mstrimas@gmail.com>

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More information about smoothr at CRAN
Permanent link

Package rSPARCS updated to version 0.0.2 with previous version 0.0.1 dated 2018-12-09

Title: Statistical Package for Analysis Related Cleaning Support
Description: To clean and analyze hospital data, and generate sets for statistical modeling.
Author: Wangjian Zhang, Zhicheng Du, Ziqiang Lin, Jijin Yao, Yanan Jin, Wayne R. Lawrence, Yuantao Hao
Maintainer: Wangjian Zhang <wzhang27@albany.edu>

Diff between rSPARCS versions 0.0.1 dated 2018-12-09 and 0.0.2 dated 2018-12-11

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Package httr updated to version 1.4.0 with previous version 1.3.1 dated 2017-08-20

Title: Tools for Working with URLs and HTTP
Description: Useful tools for working with HTTP organised by HTTP verbs (GET(), POST(), etc). Configuration functions make it easy to control additional request components (authenticate(), add_headers() and so on).
Author: Hadley Wickham [aut, cre], RStudio [cph]
Maintainer: Hadley Wickham <hadley@rstudio.com>

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Package cubature updated to version 2.0.2 with previous version 2.0.1 dated 2018-11-29

Title: Adaptive Multivariate Integration over Hypercubes
Description: R wrappers around the cubature C library of Steven G. Johnson for adaptive multivariate integration over hypercubes and the Cuba C library of Thomas Hahn for deterministic and Monte Carlo integration. Scalar and vector interfaces for cubature and Cuba routines are provided; the vector interfaces are highly recommended as demonstrated in the package vignette.
Author: Balasubramanian Narasimhan [aut, cre], Manuel Koller [ctb], Steven G. Johnson [aut], Thomas Hahn [aut], Annie Bouvier [aut], Kiên Kiêu [aut], Simen Gaure [ctb]
Maintainer: Balasubramanian Narasimhan <naras@stat.stanford.edu>

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Package MKmisc updated to version 1.2 with previous version 1.1 dated 2018-08-05

Title: Miscellaneous Functions from M. Kohl
Description: Contains several functions for statistical data analysis; e.g. for sample size and power calculations, computation of confidence intervals, and generation of similarity matrices.
Author: Matthias Kohl [aut, cre] (<https://orcid.org/0000-0001-9514-8910>)
Maintainer: Matthias Kohl <Matthias.Kohl@stamats.de>

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Package wrapr updated to version 1.8.0 with previous version 1.7.0 dated 2018-11-15

Title: Wrap R Tools for Debugging and Parametric Programming
Description: Tools for writing and debugging R code. Provides: 'let()' (converts non-standard evaluation interfaces to parametric standard evaluation interfaces, inspired by 'gtools:strmacro()' and 'base::bquote()'), '%.>%' dot-pipe (an 'S3' configurable pipe), '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>

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Package photobiology updated to version 0.9.25 with previous version 0.9.24 dated 2018-09-23

Title: Photobiological Calculations
Description: Definitions of classes, methods, operators and functions for use in photobiology and radiation meteorology and climatology. Calculation of effective (weighted) and not-weighted irradiances/doses, fluence rates, transmittance, reflectance, absorptance, absorbance and diverse ratios and other derived quantities from spectral data. Local maxima and minima. Conversion between energy- and photon-based units. Wavelength interpolation. Astronomical calculations related solar angles and day length. Colours and vision. This package is part of the 'r4photobiology' suite, Aphalo P. J. (2015) <doi:10.19232/uv4pb.2015.1.14>.
Author: Pedro J. Aphalo [aut, cre] (<https://orcid.org/0000-0003-3385-972X>), Titta K. Kotilainen [ctb] (<https://orcid.org/0000-0002-2822-9734>), Glenn Davis [ctb]
Maintainer: Pedro J. Aphalo <pedro.aphalo@helsinki.fi>

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Package RNAsmc updated to version 0.4.0 with previous version 0.3.0 dated 2018-03-19

Title: RNA Secondary Structure Module Mining, Comparison and Plotting
Description: Provides function for RNA secondary structure plotting, comparison and module mining. Given a RNA secondary structure, you can obtain stem regions, hairpin loops, internal loops, bulge loops and multibranch loops of this RNA structure using this program. They are the basic modules of RNA secondary structure. For each module you get, you can use this program to label the RNA structure with a specific color. You can also use this program to compare two RNA secondary structures to get a score that represents similarity. Reference: Reuter JS, Mathews DH (2010) <doi:10.1186/1471-2105-11-129>.
Author: Zheng HeWei
Maintainer: Zheng HeWei<zhenghw@hrbmu.edu.cn>

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Package mdsstat updated to version 0.2.1 with previous version 0.2.0 dated 2018-09-26

Title: Statistical Trending for Medical Devices Surveillance
Description: A collection of common statistical algorithms used in active surveillance of medical device events. Context includes post-market surveillance, pharmacovigilance, signal detection and trending, and regulatory reporting. Primary inputs are device-event time series. Outputs include trending results with the ability to run multiple algorithms at once. This package works well with the 'mds' package, but does not require it.
Author: Gary Chung [aut, cre]
Maintainer: Gary Chung <gchung05@gmail.com>

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Package jmv updated to version 0.9.6 with previous version 0.9.5 dated 2018-11-16

Title: The 'jamovi' Analyses
Description: A suite of common statistical methods such as descriptives, t-tests, ANOVAs, regression, correlation matrices, proportion tests, contingency tables, and factor analysis. This package is also useable from the 'jamovi' statistical spreadsheet (see <https://www.jamovi.org> for more information).
Author: Ravi Selker, Jonathon Love, Damian Dropmann
Maintainer: Jonathon Love <jon@thon.cc>

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Permanent link

Package CrossVA updated to version 0.9.4 with previous version 0.9.3 dated 2018-10-24

Title: Verbal Autopsy Data Transform for Use with Various Coding Algorithms
Description: Enables transformation of Verbal Autopsy data collected with the WHO 2016 questionnaire (versions 1.4.1 & 1.5.1) for automated coding of Cause of Death using different computer algorithms. Currently supports user-supplied mappings, and provides unvalidated, experimental-stage mapping definitions to transform to InterVA4, InterVA5, Tariff 2, and InSilicoVA. This package is made available by WHO, in collaboration with the Swiss Tropical and Public Health Institute and the Bloomberg Data for Health Initiative.
Author: Eungang Choi [aut], Sam Clark [aut], Zehang Li [aut], Nicolas Maire [aut], Jason Thomas [aut, cre]
Maintainer: Jason Thomas <jarathomas@gmail.com>

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Mon, 10 Dec 2018

Package knitr updated to version 1.21 with previous version 1.20 dated 2018-02-20

Title: A General-Purpose Package for Dynamic Report Generation in R
Description: Provides a general-purpose tool for dynamic report generation in R using Literate Programming techniques.
Author: Yihui Xie [aut, cre] (<https://orcid.org/0000-0003-0645-5666>), Adam Vogt [ctb], Alastair Andrew [ctb], Alex Zvoleff [ctb], Andre Simon [ctb] (the CSS files under inst/themes/ were derived from the Highlight package http://www.andre-simon.de), Aron Atkins [ctb], Aaron Wolen [ctb], Ashley Manton [ctb], Ben Baumer [ctb], Brian Diggs [ctb], Brian Zhang [ctb], Cassio Pereira [ctb], Christophe Dervieux [ctb], David Hugh-Jones [ctb], David Robinson [ctb], Donald Arseneau [ctb, cph] (the framed package at inst/misc/framed.sty), Doug Hemken [ctb], Duncan Murdoch [ctb], Elio Campitelli [ctb], Fabian Hirschmann [ctb], Fitch Simeon [ctb], Forest Fang [ctb], Frank E Harrell Jr [ctb] (the Sweavel package at inst/misc/Sweavel.sty), Garrick Aden-Buie [ctb], Gregoire Detrez [ctb], Hadley Wickham [ctb], Hao Zhu [ctb], Heewon Jeon [ctb], Henrik Bengtsson [ctb], Hiroaki Yutani [ctb], Ian Lyttle [ctb], Hodges Daniel [ctb], Jake Burkhead [ctb], James Manton [ctb], Jared Lander [ctb], Jason Punyon [ctb], Javier Luraschi [ctb], Jeff Arnold [ctb], Jenny Bryan [ctb], Jeremy Ashkenas [ctb, cph] (the CSS file at inst/misc/docco-classic.css), Jeremy Stephens [ctb], Jim Hester [ctb], Joe Cheng [ctb], Johannes Ranke [ctb], John Honaker [ctb], John Muschelli [ctb], Jonathan Keane [ctb], JJ Allaire [ctb], Johan Toloe [ctb], Jonathan Sidi [ctb], Joseph Larmarange [ctb], Julien Barnier [ctb], Kaiyin Zhong [ctb], Kamil Slowikowski [ctb], Karl Forner [ctb], Kevin K. Smith [ctb], Kirill Mueller [ctb], Kohske Takahashi [ctb], Lorenz Walthert [ctb], Lucas Gallindo [ctb], Martin Modrák [ctb], Michael Chirico [ctb], Michael Friendly [ctb], Michal Bojanowski [ctb], Michel Kuhlmann [ctb], Nacho Caballero [ctb], Nick Salkowski [ctb], Noam Ross [ctb], Obada Mahdi [ctb], Qiang Li [ctb], Ramnath Vaidyanathan [ctb], Richard Cotton [ctb], Robert Krzyzanowski [ctb], Romain Francois [ctb], Ruaridh Williamson [ctb], Scott Kostyshak [ctb], Sebastian Meyer [ctb], Sietse Brouwer [ctb], Simon de Bernard [ctb], Sylvain Rousseau [ctb], Taiyun Wei [ctb], Thibaut Assus [ctb], Thibaut Lamadon [ctb], Thomas Leeper [ctb], Tim Mastny [ctb], Tom Torsney-Weir [ctb], Trevor Davis [ctb], Viktoras Veitas [ctb], Weicheng Zhu [ctb], Wush Wu [ctb], Zachary Foster [ctb]
Maintainer: Yihui Xie <xie@yihui.name>

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Package drake updated to version 6.2.1 with previous version 6.1.0 dated 2018-10-26

Title: A Pipeline Toolkit for Reproducible Computation at Scale
Description: A general-purpose computational engine for data analysis, drake rebuilds intermediate data objects when their dependencies change, and it skips work when the results are already up to date. Not every execution starts from scratch, there is native support for parallel and distributed computing, and completed projects have tangible evidence that they are reproducible. Extensive documentation, from beginner-friendly tutorials to practical examples and more, is available at the reference website <https://ropensci.github.io/drake/> and the online manual <https://ropenscilabs.github.io/drake-manual/>.
Author: William Michael Landau [aut, cre] (<https://orcid.org/0000-0003-1878-3253>), Alex Axthelm [ctb], Jasper Clarkberg [ctb], Kirill Müller [ctb], Ben Marwick [rev], Peter Slaughter [rev], Ben Bond-Lamberty [ctb] (<https://orcid.org/0000-0001-9525-4633>), Eli Lilly and Company [cph]
Maintainer: William Michael Landau <will.landau@gmail.com>

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 drake-6.2.1/drake/tests/testthat/test-deprecate.R             |  105 +-
 drake-6.2.1/drake/tests/testthat/test-edge-cases.R            |   16 
 drake-6.2.1/drake/tests/testthat/test-envir.R                 |  133 ++
 drake-6.2.1/drake/tests/testthat/test-examples.R              |   81 -
 drake-6.2.1/drake/tests/testthat/test-expose-imports.R        |    4 
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 drake-6.2.1/drake/tests/testthat/test-hash.R                  |    2 
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 drake-6.2.1/drake/tests/testthat/test-lazy-load.R             |   11 
 drake-6.2.1/drake/tests/testthat/test-map-reduce.R            |   85 +
 drake-6.2.1/drake/tests/testthat/test-memory-cache.R          |   19 
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 drake-6.2.1/drake/tests/testthat/test-other-features.R        |    6 
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 drake-6.2.1/drake/tests/testthat/test-time.R                  |   62 -
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 drake-6.2.1/drake/tests/testthat/test-wildcards.R             |  134 ++
 drake-6.2.1/drake/tests/testthat/test-with-processx.R         |    4 
 drake-6.2.1/drake/vignettes/drake.Rmd                         |    7 
 221 files changed, 5050 insertions(+), 4555 deletions(-)

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