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>

Diff between rcrtan versions 0.1.0 dated 2018-08-17 and 0.1.1 dated 2018-12-19

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 MD5                           |   14 ++---
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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

New package OmnibusFisher with initial version 1.0
Package: OmnibusFisher
Type: Package
Title: A Modified Fisher’s Method to Test Overall Gene-Level Effect
Version: 1.0
Author: Qi Yan
Maintainer: Qi Yan <qiy17@pitt.edu>
Description: The separate p-values of SNPs, RNA expressions and DNA methylations are calculated by KM regression. The correlation between different omics data are taken into account. This method can be applied to either samples with all three types of omics data or samples with two types.
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
Depends: CompQuadForm, stringr
Imports: survey
RoxygenNote: 6.0.0
Collate: 'OmnibusFisher_iteration_GM.R' 'OmnibusFisher_iteration_GMR.R' 'OmnibusFisher_iteration_GR.R' 'OmnibusFisher_iteration_MR.R' 'OmnibusFisher_outer.R' 'example_data.R'
Packaged: 2018-12-10 15:52:18 UTC; qiyan
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-12-19 08:30:03 UTC

More information about OmnibusFisher 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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More information about colourvalues at CRAN
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

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 tests/testthat/test-01-data-load.R         |    3 
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 vignettes/GenEstGUI.Rmd                    |    2 
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 45 files changed, 706 insertions(+), 712 deletions(-)

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Tue, 18 Dec 2018

New package waterquality with initial version 0.2.2
Package: waterquality
Title: Satellite Derived Water Quality Detection Algorithms
Version: 0.2.2
Authors@R: c(person("Richard", "Johansen", email = "richard.johansen@uc.edu", role = c("aut", "cre"), comment = c(ORCID = "0000-0003-4287-9677")), person("Jakub", "Nowosad", email="nowosad.jakub@gmail.com", role = c("aut"), comment = c(ORCID = "0000-0002-1057-3721")), person("Molly", "Reif", email="Molly.K.Reif@usace.army.mil", role = c("aut"), comment = c(ORCID = "0000-0003-4207-1459")), person("Erich", "Emery", email="Erich.B.Emery@usace.army.mil", role = c("aut")), person("U.S. Army Corps of Engineers", role = c("fnd")))
Description: The goal of 'waterquality' is to convert satellite-reflectance imagery to a host of pre-defined water quality algorithms designed for the detection of chlorophyll-a, blue-green algae (Phycocyanin), and turbidity. This package is able to process the following sensor configurations: WorldView-2, Sentinel-2, Landsat-8, MODIS, and MERIS.
Depends: R (>= 3.4.0)
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: methods, raster, rgdal
RoxygenNote: 6.1.1
Suggests: testthat, knitr, tibble, rmarkdown, covr
URL: https://github.com/RAJohansen/waterquality
BugReports: https://github.com/RAJohansen/waterquality/issues
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-10 18:44:39 UTC; johansra
Author: Richard Johansen [aut, cre] (<https://orcid.org/0000-0003-4287-9677>), Jakub Nowosad [aut] (<https://orcid.org/0000-0002-1057-3721>), Molly Reif [aut] (<https://orcid.org/0000-0003-4207-1459>), Erich Emery [aut], U.S. Army Corps of Engineers [fnd]
Maintainer: Richard Johansen <richard.johansen@uc.edu>
Repository: CRAN
Date/Publication: 2018-12-18 23:20:03 UTC

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New package VDJgermlines with initial version 0.1
Package: VDJgermlines
Type: Package
Title: Variable, Diversity and Joining Sequences from Various Species
Version: 0.1
Date: 2018-12-10
Author: Alexander Yermanos
Maintainer: Alexander Yermanos <ayermanos@gmail.com>
Depends: R(>= 3.1.0), ape, stringdist
Description: Contains variable, diversity, and joining sequences and accompanying functions that enable both the extraction of and comparison between immune V-D-J genomic segments from a variety of species. Sources include IMGT from MP Lefranc (2009) <doi:10.1093/nar/gkn838> and Vgenerepertoire from publication DN Olivieri (2014) <doi:10.1007/s00251-014-0784-3>.
License: GPL-2
LazyData: true
Encoding: UTF-8
RoxygenNote: 5.0.1
Suggests: knitr, rmarkdown
NeedsCompilation: no
Packaged: 2018-12-10 13:36:52 UTC; ayermano
Repository: CRAN
Date/Publication: 2018-12-18 23:30:32 UTC

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New package SIGN with initial version 0.1.0
Package: SIGN
Type: Package
Title: Similarity Identification in Gene Expression
Version: 0.1.0
Date: 2018-12-02
Authors@R: c( person("Seyed Ali", "Madani Tonekaboni", , email = "ali.madanitonekaboni@mail.utoronto.ca", role = c("aut")), person("Gangesh", "Beri", , email = "gangesh.beri@uhnresearch.ca", role = c("aut")), person("Janosch", "Ortmann", , email = "janosch.ortmann@gmail.com", role = c("aut")), person("Benjamin", "Haibe-Kains", , email = "benjamin.haibe.kains@utoronto.ca", role = c("aut", "cre")) )
Description: Provides a classification framework to use expression patterns of pathways as features to identify similarity between biological samples. It provides a new measure for quantifying similarity between expression patterns of pathways.
Depends: R(>= 3.4)
License: GPL (>= 3)
Imports: stats, utils, survcomp, survival, GSVA
Encoding: UTF-8
LazyData: true
NeedsCompilation: yes
biocViews: GeneExpression, Classification, Clustering, Survival
Packaged: 2018-12-10 17:53:22 UTC; alimadani
RoxygenNote: 6.1.1
Author: Seyed Ali Madani Tonekaboni [aut], Gangesh Beri [aut], Janosch Ortmann [aut], Benjamin Haibe-Kains [aut, cre]
Maintainer: Benjamin Haibe-Kains <benjamin.haibe.kains@utoronto.ca>
Repository: CRAN
Date/Publication: 2018-12-18 23:11:47 UTC

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New package rdhs with initial version 0.6.0
Package: rdhs
Type: Package
Title: API Client and Dataset Management for the Demographic and Health Survey (DHS) Data
Version: 0.6.0
Authors@R: c(person(given = "OJ", family = "Watson", role = c("aut", "cre"), email = "oj.watson@hotmail.co.uk", comment = c(ORCID = "0000-0003-2374-0741")), person(given = "Jeff", family = "Eaton", role = "aut", comment = c(ORCID = "0000-0001-7728-728X")), person(given = "Lucy", family = "D'Agostino McGowan", role = "rev", comment = c(ORCID = "0000-0001-7297-9359")), person(given = "Duncan", family = "Gillespie", role = "rev"))
Maintainer: OJ Watson <oj.watson@hotmail.co.uk>
URL: https://ropensci.github.io/rdhs/
BugReports: https://github.com/ropensci/rdhs/issues
Description: Provides a client for (1) querying the DHS API for survey indicators and metadata (<https://api.dhsprogram.com/#/index.html>), (2) identifying surveys and datasets for analysis, (3) downloading survey datasets from the DHS website, (4) loading datasets and associate metadata into R, and (5) extracting variables and combining datasets for pooled analysis.
LazyData: TRUE
Depends: R (>= 3.3.0)
Imports: R6, httr, jsonlite, foreign, magrittr, rappdirs, digest, storr, xml2, qdapRegex, rgdal, getPass, haven, iotools
Suggests: testthat, knitr, rmarkdown, ggplot2, survey, data.table, microbenchmark
License: MIT + file LICENSE
RoxygenNote: 6.1.1
VignetteBuilder: knitr
Language: en-GB
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-12-10 19:20:04 UTC; oj
Author: OJ Watson [aut, cre] (<https://orcid.org/0000-0003-2374-0741>), Jeff Eaton [aut] (<https://orcid.org/0000-0001-7728-728X>), Lucy D'Agostino McGowan [rev] (<https://orcid.org/0000-0001-7297-9359>), Duncan Gillespie [rev]
Repository: CRAN
Date/Publication: 2018-12-18 23:10:03 UTC

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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>

Diff between r2d3 versions 0.2.2 dated 2018-05-30 and 0.2.3 dated 2018-12-18

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 12 files changed, 1521 insertions(+), 763 deletions(-)

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New package NetworkSim with initial version 0.1.0
Package: NetworkSim
Type: Package
Title: Network Comparison Based on Structural Equivalence and Graphlets
Version: 0.1.0
Date: 2018-12-11
Author: Qili Shi, Libing Shen, Qi Liao, Shun Zhang
Maintainer: Qili Shi <qili.shi@hotmail.com>
Description: Functions to evaluate pair-wise similarity of two networks especially on high-dimensional data.
Depends: R (>= 3.4.0)
Imports: igraph, incgraph
Suggests: limma, DESeq2, edgeR, org.Hs.eg.db
License: GPL-3
Encoding: UTF-8
LazyData: TRUE
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-11 08:53:16 UTC; lenovo
Repository: CRAN
Date/Publication: 2018-12-18 23:31:03 UTC

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New package MTLR with initial version 0.1.0
Package: MTLR
Type: Package
Title: Survival Prediction with Multi-Task Logistic Regression
Version: 0.1.0
Author: Humza Haider
Maintainer: Humza Haider <hshaider@ualberta.ca>
URL: https://github.com/haiderstats/MTLR
BugReports: https://github.com/haiderstats/MTLR/issues
Description: An implementation of Multi-Task Logistic Regression (MTLR) for R. This package is based on the method proposed by Yu et al. (2011) which utilized MTLR for generating individual survival curves by learning feature weights which vary across time. This model was further extended to account for left and interval censored data.
License: GPL-2 | file LICENSE
Encoding: UTF-8
LazyData: true
Imports: Rcpp (>= 0.12.18), survival (>= 2.4.0)
Suggests: ggplot2 (>= 3.0.0), reshape2 (>= 1.4.3), testthat, covr, knitr, rmarkdown
Depends: R (>= 3.4.0)
RoxygenNote: 6.1.1
LinkingTo: Rcpp, RcppArmadillo
VignetteBuilder: knitr
NeedsCompilation: yes
Packaged: 2018-12-10 17:58:19 UTC; humza
Repository: CRAN
Date/Publication: 2018-12-18 23:12:36 UTC

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New package MachineLearning with initial version 0.0.2
Package: MachineLearning
Title: Machine Learning Algorithms for Innovation in Tourism
Version: 0.0.2
Authors@R: c( person("Agustin", "Perez-Martin", email = "agustin.perez@umh.es", role = "aut", comment = c(ORCID = "0000-0003-4994-3176")), person("Agustin", "Perez-Torregrosa", email = "agustin.perez01@goumh.umh.es", role =c("cre","aut"), comment = c(ORCID = "0000-0001-5658-4795")), person("Alejandro", "Rabasa-Dolado", email = "a.rabasa@umh.es", role ="aut" , comment = c(ORCID = "0000-0002-6243-9831")), person("Nuria", "Molla-Campello", email = "nuria.molla@goumh.umh.es", role = "aut", comment = c(ORCID = "0000-0002-6448-7116")), person("Jesus Javier", "Rodriguez-Sala", email = "jesuja.rodriguez@umh.es", role = "aut", comment = c(ORCID = "0000-0002-3796-0692")), person(family = "Agencia Valenciana de Turisme", role = c("ctb", "cph", "fnd")), person(family = "Miguel Hernandez University", role = c("ctb", "cph", "fnd")) )
Description: A collection of routines created in the collaboration framework in tourism innovation between the Valencian Tourism Agency (AVT) <http://www.turisme.gva.es/opencms/opencms/turisme/es/index.jsp> and the Miguel Hernandez University. The package provides a set of machine learning tools for pattern detection, association and classification rules and feature selection even under massive data environments. Almiñana, Escudero, Pérez-Martín, Rabasa, and Santamaría (2014) <doi:10.1007/s11750-012-0264-6>.
Depends: R (>= 3.3.0)
Imports: NbClust, dplyr, formula.tools, magrittr, arules, rpart, FSelectorRcpp, crayon, ggplot2, rpart.plot
License: AGPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
Suggests: spelling, testthat
Language: en-GB
NeedsCompilation: no
Packaged: 2018-12-10 17:18:38 UTC; agustin
Author: Agustin Perez-Martin [aut] (<https://orcid.org/0000-0003-4994-3176>), Agustin Perez-Torregrosa [cre, aut] (<https://orcid.org/0000-0001-5658-4795>), Alejandro Rabasa-Dolado [aut] (<https://orcid.org/0000-0002-6243-9831>), Nuria Molla-Campello [aut] (<https://orcid.org/0000-0002-6448-7116>), Jesus Javier Rodriguez-Sala [aut] (<https://orcid.org/0000-0002-3796-0692>), Agencia Valenciana de Turisme [ctb, cph, fnd], Miguel Hernandez University [ctb, cph, fnd]
Maintainer: Agustin Perez-Torregrosa <agustin.perez01@goumh.umh.es>
Repository: CRAN
Date/Publication: 2018-12-18 23:12:17 UTC

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New package fuzzySim with initial version 2.0
Package: fuzzySim
Type: Package
Title: Fuzzy Similarity in Species Distributions
Version: 2.0
Date: 2018-12-05
Author: Barbosa A.M.
Maintainer: A. Marcia Barbosa <barbosa@uevora.pt>
Suggests: maptools, parallel, PBSmapping, sp, tools, raster
Description: Functions to calculate fuzzy versions of species' occurrence patterns based on presence-absence data (including inverse distance interpolation, trend surface analysis and prevalence-independent favourability GLM), and pair-wise fuzzy similarity (based on fuzzy versions of commonly used similarity indices) among those occurrence patterns. Includes also functions for model comparison (overlap and fuzzy similarity, loss or gain), and for data preparation, such as obtaining unique abbreviations of species names, converting species lists (long format) to presence-absence tables (wide format), transposing part of a data frame, assessing the false discovery rate, or analysing and dealing with multicollinearity among variables. Includes also sample datasets for providing practical examples.
License: GPL-3
NeedsCompilation: no
Packaged: 2018-12-10 18:39:50 UTC; marcia
Depends: R (>= 2.10)
Repository: CRAN
Date/Publication: 2018-12-18 23:10:32 UTC

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New package fluspect with initial version 1.0.0
Package: fluspect
Type: Package
Title: Fluspect-B
Version: 1.0.0
Author: Alberto Hornero, Nastassia Vilfan, Christiaan van der Tol, Onno Muller, Uwe Rascher, Wouter Verhoef
Maintainer: Alberto Hornero <alberto@hornero.es>
Description: A model for leaf fluorescence, reflectance and transmittance spectra. It implements the model introduced by Vilfan et al. (2016) <DOI:10.1016/j.rse.2016.09.017>. Fluspect-B calculates the emission of ChlF on both the illuminated and shaded side of the leaf. Other input parameters are chlorophyll and carotenoid concentrations, leaf water, dry matter and senescent material (brown pigments) content, leaf mesophyll structure parameter and ChlF quantum efficiency for the two photosystems, PS-I and PS-II.
License: GPL-3
Encoding: UTF-8
Depends: R (>= 2.10)
Imports: pracma, utils
LazyData: false
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-10 12:19:06 UTC; ahornero
Repository: CRAN
Date/Publication: 2018-12-18 23:30:05 UTC

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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>

Diff between ritis versions 0.7.2 dated 2018-05-20 and 0.7.6 dated 2018-12-18

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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>

Diff between drtmle versions 1.0.3 dated 2018-07-02 and 1.0.4 dated 2018-12-18

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New package congressbr with initial version 0.1.5
Package: congressbr
Type: Package
Title: Downloads, Unpacks and Tidies Legislative Data from the Brazilian Federal Senate and Chamber of Deputies
Version: 0.1.5
Authors@R: c( person(given = "Robert", family = "McDonnell", email = "mcdonnell.robert5@gmail.com", role = c("aut", "cre")), person(given = "Guilherme", family = "Jardim Duarte", email = "gjardimduarte@gmail.com", role = "aut"), person(given = "Danilo", family = "Freire", email = "danilofreire@gmail.com", role = "aut"), person(given = "Julio", family = "Trecenti", role = "aut") )
Description: Downloads and tidies data from the Brazilian Federal Senate and Chamber of Deputies Application Programming Interfaces available at <http:// legis.senado.gov.br/dadosabertos/> and <http://www.camara.leg.br/SitCamaraWS/> respectively.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 3.0)
Imports: dplyr (>= 0.5.0), purrr (>= 0.2.2), xml2 (>= 1.0.0), httr(>= 1.2.1), lubridate (>= 1.6.0), magrittr (>= 1.5), stringi (>= 1.1.2), tidyr (>= 0.6.0), stringr (>= 1.1.0), tibble (>= 1.2), pscl (>= 1.4.9), glue (>= 0.0.1), progress (>= 0.0.1)
RoxygenNote: 6.1.1
Suggests: devtools, ggplot2, httptest, knitr, rmarkdown, covr
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-18 20:50:33 UTC; robert
Author: Robert McDonnell [aut, cre], Guilherme Jardim Duarte [aut], Danilo Freire [aut], Julio Trecenti [aut]
Maintainer: Robert McDonnell <mcdonnell.robert5@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-18 22:30:17 UTC

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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>

Diff between httpuv versions 1.4.5 dated 2018-07-19 and 1.4.5.1 dated 2018-12-18

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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>

Diff between sjPlot versions 2.6.1 dated 2018-10-14 and 2.6.2 dated 2018-12-18

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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>

Diff between blocksdesign versions 3.1 dated 2018-10-18 and 3.2 dated 2018-12-18

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New package readABF with initial version 1.0.1
Package: readABF
Title: Loads Axon Binary Files
Version: 1.0.1
Authors@R: c(person("Stanislav", "Syekirin", role = c("aut", "cre"), email = "syekirin@gmail.com"), person("Florian", "Pein", role = "ctb", email = "fpein@uni-goettingen.de"))
Description: Loads Axon Binary Files (both 'ABF' and 'ABF2') created by Axon Instruments/Molecular Devices software such as 'pClamp'.
Depends: R (>= 3.2.0)
License: GPL-3
Imports: graphics, methods
Suggests: testthat
RoxygenNote: 6.0.1
NeedsCompilation: no
Packaged: 2018-12-10 08:57:38 UTC; zabolekar
Author: Stanislav Syekirin [aut, cre], Florian Pein [ctb]
Maintainer: Stanislav Syekirin <syekirin@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-18 16:40:03 UTC

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New package probably with initial version 0.0.1
Package: probably
Version: 0.0.1
Title: Tools for Post-Processing Class Probability Estimates
Description: Models can be improved by post-processing class probabilities, by: recalibration, conversion to hard probabilities, assessment of equivocal zones, and other activities. 'probably' contains tools for conducting these operations.
Authors@R: c( person("Max", "Kuhn", , "max@rstudio.com", c("aut", "cre")), person("Davis", "Vaughan", , "davis@rstudio.com", c("aut")), person("RStudio", role = "cph"))
Maintainer: Max Kuhn <max@rstudio.com>
URL: https://github.com/tidymodels/probably/
BugReports: https://github.com/tidymodels/probably/issues
License: GPL-2
Encoding: UTF-8
LazyData: true
ByteCompile: true
RoxygenNote: 6.1.0.9000
Depends: R (>= 2.10)
Imports: dplyr, generics, rlang, tidyselect, vctrs, yardstick
Suggests: testthat, covr, knitr, rmarkdown, parsnip, ggplot2
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-09 22:00:37 UTC; davis
Author: Max Kuhn [aut, cre], Davis Vaughan [aut], RStudio [cph]
Repository: CRAN
Date/Publication: 2018-12-18 16:40:05 UTC

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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>

Diff between EpiModel versions 1.7.0 dated 2018-11-21 and 1.7.2 dated 2018-12-18

 DESCRIPTION                          |   18 +++--
 MD5                                  |   53 +++++++++------
 NAMESPACE                            |    5 +
 NEWS.md                              |   27 ++++++++
 R/EpiModel-package.r                 |    6 +
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 R/as.data.frame.R                    |    2 
 R/control.R                          |   27 +++++++-
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 R/merge.R                            |    4 -
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 R/netsim.R                           |    4 +
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 R/utils.R                            |   52 +++++++++++++++
 R/verbose.R                          |  118 +++--------------------------------
 build/vignette.rds                   |binary
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 inst/shiny/epidcm/server.R           |    2 
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 inst/shiny/epinet/server.R           |    4 -
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 29 files changed, 434 insertions(+), 187 deletions(-)

More information about EpiModel at CRAN
Permanent link

New package easyalluvial with initial version 0.1.7
Package: easyalluvial
Title: Generate Alluvial Plots with a Single Line of Code
Version: 0.1.7
Authors@R: person( "Bjoern", "Koneswarakantha", role = c("aut","cre"), email = "datistics@gmail.com", comment = c(ORCID = " 0000-0003-4585-7799") )
URL: https://github.com/erblast/easyalluvial
Description: Alluvial plots are similar to sankey diagrams and visualise categorical data over multiple dimensions as flows. (Rosvall M, Bergstrom CT (2010) Mapping Change in Large Networks. PLoS ONE 5(1): e8694. <doi:10.1371/journal.pone.0008694> Their graphical grammar however is a bit more complex then that of a regular x/y plots. The 'ggalluvial' package made a great job of translating that grammar into 'ggplot2' syntax and gives you many option to tweak the appearance of an alluvial plot, however there still remains a multi-layered complexity that makes it difficult to use 'ggalluvial' for explorative data analysis. 'easyalluvial' provides a simple interface to this package that allows you to produce a decent alluvial plot from any dataframe in either long or wide format from a single line of code while also handling continuous data. It is meant to allow a quick visualisation of entire dataframes with a focus on different colouring options that can make alluvial plots a great tool for data exploration.
License: CC0
Encoding: UTF-8
LazyData: true
Depends: R(>= 2.10)
Suggests: testthat, covr, ISLR, nycflights13
RoxygenNote: 6.1.1
Imports: purrr , tidyr , dplyr , forcats , ggalluvial , ggplot2 , RColorBrewer , recipes , rlang , stringr , magrittr , tibble
Language: en-US
NeedsCompilation: no
Packaged: 2018-12-10 00:19:39 UTC; erbla
Author: Bjoern Koneswarakantha [aut, cre] (<https://orcid.org/ 0000-0003-4585-7799>)
Maintainer: Bjoern Koneswarakantha <datistics@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-18 16:50:03 UTC

More information about easyalluvial at CRAN
Permanent link

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>

Diff between dbarts versions 0.9-5 dated 2018-07-07 and 0.9-7 dated 2018-12-18

 DESCRIPTION                              |    8 +--
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 NAMESPACE                                |    3 -
 R/A_class.R                              |    2 
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 R/plot.R                                 |   76 ++++++++++++++++++++++++++++---
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 man/bart.Rd                              |   12 ++--
 man/rbart.Rd                             |   20 ++++++--
 src/Makevars.in                          |   76 +++++++++++--------------------
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 src/makeModelMatrixFromDataFrame.c       |    6 --
 src/rc/Makefile                          |    7 +-
 tests/testthat/test-09-predict.R         |   14 +++++
 tests/testthat/test-14-rbart.R           |    3 -
 33 files changed, 385 insertions(+), 244 deletions(-)

More information about dbarts at CRAN
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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>

Diff between CornerstoneR versions 1.0.0 dated 2018-12-16 and 1.0.1 dated 2018-12-18

 DESCRIPTION                          |   11 ++++----
 MD5                                  |   17 +++++++------
 NEWS.md                              |    6 +++-
 R/helper.R                           |    6 +---
 R/randomForest.R                     |    4 +++
 man/randomForest.Rd                  |    7 ++++-
 tests/testthat/Rplots.pdf            |binary
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More information about CornerstoneR at CRAN
Permanent link

New package cansim with initial version 0.2.2
Package: cansim
Type: Package
Title: Accessing Statistics Canada Data Table and Vectors
Version: 0.2.2
Authors@R: c( person("Jens", "von Bergmann", email = "jens@mountainmath.ca", role = c("cre")), person("Dmitry", "Shkolnik", email = "shkolnikd@gmail.com", role = c("aut")))
Maintainer: Jens von Bergmann <jens@mountainmath.ca>
Description: Searches for, accesses, and retrieves new-format and old-format Statistics Canada data tables, as well as individual vectors, as tidy data frames. This package deals with encoding issues, allows for bilingual English or French language data retrieval, and bundles convenience functions to make it easier to work with retrieved table data. Optional caching features are provided.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Depends: R (>= 2.10)
Imports: dplyr (>= 0.7), httr (>= 1.0.0), readr, rlang, xml2, rvest, stringr, purrr, tibble, utils, jsonlite
RoxygenNote: 6.1.1
Suggests: knitr, rmarkdown, scales, tidyr, ggplot2
URL: https://github.com/mountainMath/cansim, https://mountainmath.github.io/cansim/
BugReports: https://github.com/mountainMath/cansim/issues
VignetteBuilder: knitr
Language: en-CA
NeedsCompilation: no
Packaged: 2018-12-10 06:40:09 UTC; jens
Author: Jens von Bergmann [cre], Dmitry Shkolnik [aut]
Repository: CRAN
Date/Publication: 2018-12-18 16:40:14 UTC

More information about cansim at CRAN
Permanent link

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 
 MD5                                                                                |   62 +-
 NAMESPACE                                                                          |   12 
 NEWS.md                                                                            |    9 
 R/coefficient_plot.R                                                               |only
 R/ff_interaction.R                                                                 |   17 
 R/ff_label.R                                                                       |only
 R/ff_plot.R                                                                        |only
 R/finalfit.R                                                                       |    3 
 R/finalfit_internal_functions.R                                                    |   85 +++
 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 
 inst/doc/bootstrap.html                                                            |   22 -
 inst/doc/export.html                                                               |   47 +-
 inst/doc/missing.html                                                              |   36 -
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 man/compoundpipe.Rd                                                                |only
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 man/extract_variable_label.Rd                                                      |   12 
 man/ff_interaction.Rd                                                              |    4 
 man/ff_label.Rd                                                                    |    9 
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 man/ff_relabel.Rd                                                                  |only
 man/fit2df.Rd                                                                      |    2 
 man/hr_plot.Rd                                                                     |    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 CpDyna (with last version 1.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-12-03 1.0

Permanent link
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

 DESCRIPTION                       |    8 +--
 MD5                               |   53 +++++++++++-----------
 NAMESPACE                         |    2 
 NEWS.md                           |    6 ++
 R/attribution.R                   |    2 
 R/deprecated.R                    |   20 --------
 R/sentiment_engines.R             |   90 ++++++++++++++++++++++++++++++++------
 R/sentocorpus.R                   |   16 +++---
 R/sentolexicons.R                 |    6 +-
 R/sentomeasures_main.R            |   31 +++++--------
 R/sentometrics.R                  |   26 +++++-----
 R/sentomodel.R                    |   10 ++--
 README.md                         |    2 
 man/add_features.Rd               |    6 +-
 man/attributions.Rd               |    2 
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 man/sento_model.Rd                |    4 -
 man/sentometrics-deprecated.Rd    |   18 -------
 man/sentometrics-package.Rd       |   22 ++++-----
 man/to_sentiment.Rd               |    3 +
 tests/testthat/test_aggregation.R |   18 +++++--
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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

 DESCRIPTION  |   10 +++++-----
 MD5          |    4 ++--
 R/knearest.R |   12 +++++++-----
 3 files changed, 14 insertions(+), 12 deletions(-)

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New package sensitivityCalibration with initial version 0.0.1
Package: sensitivityCalibration
Type: Package
Title: A Calibrated Sensitivity Analysis for Matched Observational Studies
Version: 0.0.1
Author: Bo Zhang
Maintainer: Bo Zhang <bozhan@wharton.upenn.edu>
Description: Implements the calibrated sensitivity analysis approach for matched observational studies. Our sensitivity analysis framework views matched sets as drawn from a super-population. The unmeasured confounder is modeled as a random variable. We combine matching and model-based covariate-adjustment methods to estimate the treatment effect. The hypothesized unmeasured confounder enters the picture as a missing covariate. We adopt a state-of-art Expectation Maximization (EM) algorithm to handle this missing covariate problem in generalized linear models (GLMs). As our method also estimates the effect of each observed covariate on the outcome and treatment assignment, we are able to calibrate the unmeasured confounder to observed covariates. Zhang, B., Small, D. S. (2018). <arXiv:1812.00215>.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: ggplot2, relaimpo, splitstackshape, ggrepel, stringi, plotly
NeedsCompilation: no
Packaged: 2018-12-09 20:48:12 UTC; ASUS
Repository: CRAN
Date/Publication: 2018-12-18 11:20:06 UTC

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New package preputils with initial version 1.0.2
Package: preputils
Type: Package
Title: Utilities for Preparation of Data Analysis
Version: 1.0.2
Date: 2018-12-03
Author: Josef Frank
Maintainer: Josef Frank <josef.frank@gmx.ch>
Description: Miscellaneous small utilities are provided to mitigate issues with messy, inconsistent or high dimensional data and help for preprocessing and preparing analyses.
Imports: data.table
License: GPL-3
Suggests: knitr, rmarkdown
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-09 23:38:32 UTC; josef
Repository: CRAN
Date/Publication: 2018-12-18 11:30:03 UTC

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New package kuiper.2samp with initial version 1.0
Package: kuiper.2samp
Title: Two-Sample Kuiper Test
Version: 1.0
Author: Ying Ruan [aut, cre]
Maintainer: Ying Ruan <y.ruan.16@ucl.ac.uk>
Description: This function performs the two-sample Kuiper test to assess the anomaly of continuous, one-dimensional probability distributions. References used for this method are (1). Kuiper, N. H. (1960). <DOI:10.1016/S1385-7258(60)50006-0> and (2). Paltani, S. (2004). <DOI:10.1051/0004-6361:20034220>.
Depends: R (>= 3.3.1)
License: AGPL-3
LazyData: true
NeedsCompilation: no
Packaged: 2018-12-09 17:36:35 UTC; Ying Taylor Ruan
Repository: CRAN
Date/Publication: 2018-12-18 11:20:09 UTC

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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>

Diff between prettyGraphs versions 2.1.5 dated 2013-12-10 and 2.1.6 dated 2018-12-18

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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>

Diff between PELVIS versions 1.0.4 dated 2018-08-05 and 1.0.5 dated 2018-12-18

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New package pcmabc with initial version 1.0
Package: pcmabc
Type: Package
Title: Approximate Bayesian Computations for Phylogenetic Comparative Methods
Version: 1.0
Date: 2018-12-09
Author: Krzysztof Bartoszek <bartoszekkj@gmail.com>, Pietro Lio'
Maintainer: Krzysztof Bartoszek <bartoszekkj@gmail.com>
Description: Fits by ABC, the parameters of a stochastic process modelling the phylogeny and evolution of a suite of traits following the tree. The user may define an arbitrary Markov process for the trait and phylogeny. Importantly, trait-dependent speciation models are handled and fitted to data.
Depends: R(>= 2.9.1)
Imports: ape (>= 3.0.6), distory, geiger, graphics, methods, mvSLOUCH, phangorn, stats, TreeSim, treespace, utils, yuima
License: GPL (>= 2) | file LICENCE
LazyLoad: yes
Collate: ABCdist.R ABCmessage.R ABC.R ABCupdate.R draw.R getTipSample.R rates.R simsde.R simtree.R
Packaged: 2018-12-09 20:22:33 UTC; kbart
NeedsCompilation: no
Repository: CRAN
Date/Publication: 2018-12-18 10:30:03 UTC

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New package metaRMST with initial version 1.0.0
Package: metaRMST
Title: Meta-Analysis of RMSTD
Version: 1.0.0
Author: Isabelle Weir [aut, cre], Lu Tian [aut], Ludovic Trinquart [aut]
Maintainer: Isabelle Weir <iweir@bu.edu>
URL: https://github.com/iweir/metaRMST
Description: R implementation of a multivariate meta-analysis of randomized controlled trials (RCT) with the difference in restricted mean survival times (RMSTD). Use this package with individual patient level data from an RCT for a time-to-event outcome to determine combined effect estimates according to 4 methods: 1) a univariate meta-analysis using observed treatment effects, 2) a univariate meta-analysis using effects predicted by fitted Royston-Parmar flexible parametric models, 3) multivariate meta-analysis with analytically derived covariance, 4) multivariate meta-analysis with bootstrap derived covariance. This package computes all combined effects and provides an RMSTD curve with combined effect estimates and their confidence intervals.
Depends: R (>= 3.4.0), rstpm2
Imports: mvmeta, meta, survival, survRM2, graphics
License: GPL-2
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.0
NeedsCompilation: no
Packaged: 2018-12-09 20:28:46 UTC; Isabelle
Repository: CRAN
Date/Publication: 2018-12-18 10:30:06 UTC

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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>

Diff between dynRB versions 0.13 dated 2018-07-13 and 0.15 dated 2018-12-18

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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>

Diff between cubature versions 2.0.2 dated 2018-12-11 and 2.0.3 dated 2018-12-18

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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>

Diff between CRF versions 0.3-16 dated 2018-05-07 and 0.4-0 dated 2018-12-18

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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>

Diff between ChaosGame versions 0.3 dated 2017-07-20 and 0.4 dated 2018-12-18

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 3 files changed, 9 insertions(+), 9 deletions(-)

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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>

Diff between quantreg versions 5.36 dated 2018-05-29 and 5.38 dated 2018-12-18

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New package LabRS with initial version 0.1.0
Package: LabRS
Type: Package
Title: Laboratorio di "Ricerca Sociale con R"
Version: 0.1.0
Author: Agnese Vardanega
Maintainer: Agnese Vardanega <avardanega@unite.it>
URL: https://www.agnesevardanega.eu/
Depends: knitr
Suggests: Rcmdr
Description: Dati, scripts e funzioni per il libro "Ricerca sociale con R. Concetti e funzioni base per la ricerca sociale" (Datasets, scripts and functions to support the book "Ricerca sociale con R. Concetti e funzioni base per la ricerca sociale").
License: GPL (>= 3)
Encoding: UTF-8
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-11-29 15:43:44 UTC; avard
Repository: CRAN
Date/Publication: 2018-12-18 09:10:09 UTC

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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>

Diff between Corbi versions 0.4-2 dated 2017-05-03 and 0.4-3 dated 2018-12-18

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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>

Diff between breathtestcore versions 0.4.5 dated 2018-10-17 and 0.4.6 dated 2018-12-18

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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>

Diff between adegraphics versions 1.0-12 dated 2018-08-31 and 1.0-15 dated 2018-12-18

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Mon, 17 Dec 2018

New package textrecipes with initial version 0.0.1
Package: textrecipes
Title: Extra 'Recipes' for Text Processing
Version: 0.0.1
Authors@R: person(given = "Emil", family = "Hvitfeldt", role = c("aut", "cre"), email = "emilhhvitfeldt@gmail.com")
Description: Converting text to numerical features requires specifically created procedures, which are implemented as steps according to the 'recipes' package. These steps allows for tokenization, filtering, counting (tf and tfidf) and feature hashing.
License: MIT + file LICENSE
Encoding: UTF-8
SystemRequirements: GNU make, C++11
LazyData: true
URL: https://github.com/tidymodels/textrecipes
BugReports: https://github.com/tidymodels/textrecipes/issues
Depends: R (>= 2.10), recipes (>= 0.1.4)
Suggests: covr, testthat, knitr, rmarkdown
RoxygenNote: 6.1.0.9000
Imports: generics, rlang, tokenizers, dplyr, tibble, purrr, SnowballC, stopwords, magrittr, stringr, text2vec
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-09 17:47:21 UTC; rstudio-user
Author: Emil Hvitfeldt [aut, cre]
Maintainer: Emil Hvitfeldt <emilhhvitfeldt@gmail.com>
Repository: CRAN
Date/Publication: 2018-12-17 23:30:03 UTC

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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>

Diff between rfUtilities versions 2.1-3 dated 2018-02-21 and 2.1-4 dated 2018-12-17

 rfUtilities-2.1-3/rfUtilities/R/rfu.news.R              |only
 rfUtilities-2.1-3/rfUtilities/R/zzz.R                   |only
 rfUtilities-2.1-3/rfUtilities/inst/NEWS                 |only
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 rfUtilities-2.1-4/rfUtilities/DESCRIPTION               |   11 -
 rfUtilities-2.1-4/rfUtilities/MD5                       |   45 +++---
 rfUtilities-2.1-4/rfUtilities/NAMESPACE                 |    2 
 rfUtilities-2.1-4/rfUtilities/NEWS                      |only
 rfUtilities-2.1-4/rfUtilities/R/accuracy.R              |  101 ++++++++------
 rfUtilities-2.1-4/rfUtilities/R/plot.rf.modelSel.R      |   10 -
 rfUtilities-2.1-4/rfUtilities/R/print.accuracy.R        |    1 
 rfUtilities-2.1-4/rfUtilities/R/rf.classBalance.R       |   15 +-
 rfUtilities-2.1-4/rfUtilities/R/rf.combine.R            |   10 -
 rfUtilities-2.1-4/rfUtilities/R/rf.crossValidation.R    |  112 +++++++++-------
 rfUtilities-2.1-4/rfUtilities/R/rf.modelSel.R           |   16 +-
 rfUtilities-2.1-4/rfUtilities/R/rf.partial.ci.R         |    6 
 rfUtilities-2.1-4/rfUtilities/R/rf.significance.R       |   40 ++---
 rfUtilities-2.1-4/rfUtilities/man/accuracy.Rd           |    5 
 rfUtilities-2.1-4/rfUtilities/man/logLoss.Rd            |    3 
 rfUtilities-2.1-4/rfUtilities/man/rf.classBalance.Rd    |    5 
 rfUtilities-2.1-4/rfUtilities/man/rf.combine.Rd         |    9 -
 rfUtilities-2.1-4/rfUtilities/man/rf.crossValidation.Rd |    4 
 rfUtilities-2.1-4/rfUtilities/man/rf.modelSel.Rd        |   16 +-
 rfUtilities-2.1-4/rfUtilities/man/rf.partial.ci.Rd      |    3 
 rfUtilities-2.1-4/rfUtilities/man/rf.partial.prob.Rd    |    5 
 rfUtilities-2.1-4/rfUtilities/man/rf.significance.Rd    |   55 ++++---
 26 files changed, 270 insertions(+), 204 deletions(-)

More information about rfUtilities at CRAN
Permanent link

New package qcv with initial version 1.0
Package: qcv
Title: Quantifying Construct Validity
Version: 1.0
Authors@R: c( person("R. Michael", "Furr", role = c("aut", "cre"), email = "FurrRM@wfu.edu"), person("Sarah", "Heuckeroth", role = "aut", email = "heucsa16@wfu.edu"))
Author: R. Michael Furr [aut, cre], Sarah Heuckeroth [aut]
Maintainer: R. Michael Furr <FurrRM@wfu.edu>
Date: 2018-11-26
Description: Primarily, the 'qcv' package computes key indices related to the Quantifying Construct Validity procedure (QCV; Westen & Rosenthal, 2003 <doi:10.1037/0022-3514.84.3.608>; see also Furr & Heuckeroth, in press). The qcv() function is the heart of the 'qcv' package, but additional functions in the package provide useful ancillary information related to the QCV procedure.
Depends: R (>= 3.5.1.0)
Imports: graphics, stats
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-09 16:43:29 UTC; furrrm
Repository: CRAN
Date/Publication: 2018-12-17 23:30:07 UTC

More information about qcv at CRAN
Permanent link

New package MVTests with initial version 1.0
Package: MVTests
Type: Package
Title: Multivariate Hypothesis Tests
Version: 1.0
Date: 2018-12-09
Author: Hasan BULUT
Maintainer: Hasan BULUT <hasan.bulut@omu.edu.tr>
Description: Multivariate hypothesis tests and the confidence intervals. This package can be used for hypothesis tests which are The Hotelling T Square Tests (One-Sample, Two Independent Samples, Paired Samples), The One Way MANOVA, The Multivariate Shapiro-Wilk Test for Multivariate Normality Test, The Bartlett Test for One Sample Covariance Matrix, The Box-M Test and The Bartlett's Sphericity Test.
Depends: R (>= 2.0), stats, matrixcalc
LazyData: true
License: GPL-3
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-09 18:15:51 UTC; user
Repository: CRAN
Date/Publication: 2018-12-17 23:20:20 UTC

More information about MVTests at CRAN
Permanent link

New package jvcoords with initial version 1.0.2
Package: jvcoords
Type: Package
Title: Principal Component Analysis (PCA) and Whitening
Version: 1.0.2
Date: 2018-12-09
Authors@R: person("Jochen", "Voss", email="voss@seehuhn.de", role=c("aut", "cre"), comment = c(ORCID = "0000-0002-2323-3814"))
License: GPL-3
URL: https://github.com/seehuhn/jvcoords
Description: Provides functions to standardize and whiten data, and to perform Principal Component Analysis (PCA). The main advantage of this package over alternatives like prcomp() is, that jvcoords makes it easy to convert (additional) data between the original and the transformed coordinates. The package also provides a class coords, which can represent affine coordinate transformations. This class forms the basis of the transformations provided by the package, but can also be used independently. The implementation has been optimized to be of comparable speed (and sometimes even faster) than existing alternatives.
NeedsCompilation: no
Packaged: 2018-12-09 18:38:07 UTC; voss
Author: Jochen Voss [aut, cre] (<https://orcid.org/0000-0002-2323-3814>)
Maintainer: Jochen Voss <voss@seehuhn.de>
Repository: CRAN
Date/Publication: 2018-12-17 23:20:04 UTC

More information about jvcoords at CRAN
Permanent link

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>

Diff between geometa versions 0.3-0 dated 2018-08-22 and 0.4-0 dated 2018-12-17

 DESCRIPTION                                           |   10 
 MD5                                                   |  318 ++++++++++--------
 NAMESPACE                                             |   26 +
 R/GMLAbstractCoverage.R                               |only
 R/GMLAbstractDiscreteCoverage.R                       |only
 R/GMLAbstractFeature.R                                |only
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 R/GMLVerticalCRS.R                                    |only
 R/ISOAbstractObject.R                                 |  284 ++++++++++++----
 R/ISOCitation.R                                       |   24 +
 R/ISOCodelist.R                                       |   14 
 R/ISOMetadata.R                                       |    8 
 R/ISOMetadataNamespace.R                              |    4 
 R/geometa.R                                           |    4 
 README.md                                             |    3 
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 tests/testthat/test_GMLOperationMethod.R              |    6 
 tests/testthat/test_GMLOperationParameter.R           |    9 
 tests/testthat/test_GMLParameterValue.R               |   14 
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 tests/testthat/test_GMLTimePeriod.R                   |    3 
 tests/testthat/test_GMLUnitDefinition.R               |   12 
 tests/testthat/test_ISOAddress.R                      |    3 
 tests/testthat/test_ISOAggregateInformation.R         |    3 
 tests/testthat/test_ISOAnchor.R                       |    3 
 tests/testthat/test_ISOAssociationRole.R              |    3 
 tests/testthat/test_ISOBand.R                         |    3 
 tests/testthat/test_ISOBaseBoolean.R                  |    3 
 tests/testthat/test_ISOBaseCharacterString.R          |    3 
 tests/testthat/test_ISOBaseDate.R                     |    3 
 tests/testthat/test_ISOBaseDateTime.R                 |    3 
 tests/testthat/test_ISOBaseDecimal.R                  |    5 
 tests/testthat/test_ISOBaseInteger.R                  |    3 
 tests/testthat/test_ISOBaseReal.R                     |    3 
 tests/testthat/test_ISOBinding.R                      |    3 
 tests/testthat/test_ISOBoundAssociationRole.R         |    3 
 tests/testthat/test_ISOBoundFeatureAttribute.R        |    3 
 tests/testthat/test_ISOBoundingPolygon.R              |    3 
 tests/testthat/test_ISOBrowseGraphic.R                |    3 
 tests/testthat/test_ISOCarrierOfCharacteristics.R     |    3 
 tests/testthat/test_ISOCitation.R                     |    3 
 tests/testthat/test_ISOConformanceResult.R            |    3 
 tests/testthat/test_ISOConstraint.R                   |    3 
 tests/testthat/test_ISOConstraints.R                  |    3 
 tests/testthat/test_ISOContact.R                      |    3 
 tests/testthat/test_ISOCoupledResource.R              |    3 
 tests/testthat/test_ISOCoverageDescription.R          |    3 
 tests/testthat/test_ISODataIdentification.R           |    3 
 tests/testthat/test_ISODataQuality.R                  |    3 
 tests/testthat/test_ISODataQualityAbstractElement.R   |    3 
 tests/testthat/test_ISODate.R                         |    3 
 tests/testthat/test_ISODefinitionReference.R          |    3 
 tests/testthat/test_ISODefinitionSource.R             |    3 
 tests/testthat/test_ISODigitalTransferOptions.R       |    3 
 tests/testthat/test_ISODimension.R                    |    2 
 tests/testthat/test_ISODistribution.R                 |    3 
 tests/testthat/test_ISODistributor.R                  |    3 
 tests/testthat/test_ISODomainConsistency.R            |    3 
 tests/testthat/test_ISOExtendedElementInformation.R   |    3 
 tests/testthat/test_ISOExtent.R                       |    3 
 tests/testthat/test_ISOFeatureAssociation.R           |    3 
 tests/testthat/test_ISOFeatureAttribute.R             |    3 
 tests/testthat/test_ISOFeatureCatalogue.R             |    2 
 tests/testthat/test_ISOFeatureCatalogueDescription.R  |    4 
 tests/testthat/test_ISOFeatureOperation.R             |    3 
 tests/testthat/test_ISOFeatureType.R                  |    3 
 tests/testthat/test_ISOFileName.R                     |    3 
 tests/testthat/test_ISOFormat.R                       |    3 
 tests/testthat/test_ISOGeographicBoundingBox.R        |    3 
 tests/testthat/test_ISOGeographicDescription.R        |    3 
 tests/testthat/test_ISOGeometricObjects.R             |    3 
 tests/testthat/test_ISOGeoreferenceable.R             |    5 
 tests/testthat/test_ISOGridSpatialRepresentation.R    |    3 
 tests/testthat/test_ISOIdentifier.R                   |    3 
 tests/testthat/test_ISOInheritanceRelation.R          |    3 
 tests/testthat/test_ISOKeywords.R                     |    3 
 tests/testthat/test_ISOLegalConstraints.R             |    3 
 tests/testthat/test_ISOLineage.R                      |    3 
 tests/testthat/test_ISOListedValue.R                  |    3 
 tests/testthat/test_ISOLocalName.R                    |    3 
 tests/testthat/test_ISOMaintenanceInformation.R       |    3 
 tests/testthat/test_ISOMeasure.R                      |    2 
 tests/testthat/test_ISOMemberName.R                   |    3 
 tests/testthat/test_ISOMetaIdentifier.R               |    3 
 tests/testthat/test_ISOMetadata.R                     |    1 
 tests/testthat/test_ISOMetadataExtensionInformation.R |    3 
 tests/testthat/test_ISOMimeFileType.R                 |    3 
 tests/testthat/test_ISOMultiplicity.R                 |    3 
 tests/testthat/test_ISOMultiplicityRange.R            |    3 
 tests/testthat/test_ISOOnlineResource.R               |    3 
 tests/testthat/test_ISOOperationMetadata.R            |    3 
 tests/testthat/test_ISOParameter.R                    |    3 
 tests/testthat/test_ISOPositionalAccuracy.R           |    8 
 tests/testthat/test_ISOProcessStep.R                  |    3 
 tests/testthat/test_ISOPropertyType.R                 |    3 
 tests/testthat/test_ISORangeDimension.R               |    3 
 tests/testthat/test_ISORecord.R                       |    3 
 tests/testthat/test_ISORecordType.R                   |    3 
 tests/testthat/test_ISOReferenceIdentifier.R          |    3 
 tests/testthat/test_ISOReferenceSystem.R              |    3 
 tests/testthat/test_ISORepresentativeFraction.R       |    3 
 tests/testthat/test_ISOResponsibleParty.R             |    3 
 tests/testthat/test_ISOScope.R                        |    3 
 tests/testthat/test_ISOSecurityConstraints.R          |    3 
 tests/testthat/test_ISOServiceIdentification.R        |    9 
 tests/testthat/test_ISOSource.R                       |    5 
 tests/testthat/test_ISOSpatialTemporalExtent.R        |    3 
 tests/testthat/test_ISOStandardOrderProcess.R         |    3 
 tests/testthat/test_ISOTelephone.R                    |    3 
 tests/testthat/test_ISOTemporalExtent.R               |    3 
 tests/testthat/test_ISOTypeName.R                     |    3 
 tests/testthat/test_ISOURL.R                          |    3 
 tests/testthat/test_ISOUnlimitedInteger.R             |    3 
 tests/testthat/test_ISOVectorSpatialRepresentation.R  |    3 
 tests/testthat/test_ISOVerticalExtent.R               |    3 
 188 files changed, 879 insertions(+), 338 deletions(-)

More information about geometa at CRAN
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New package FLAME with initial version 1.0.0
Package: FLAME
Type: Package
Title: A Fast Large-Scale Almost Matching Exactly Approach to Causal Inference
Version: 1.0.0
Authors@R: c(person("Chia-Rui (Jerry)", "Chang", role=c("aut", "cre"), email = "chiarui424@gmail.com"), person("Cynthia", "Rudin", role = c("aut"), email = "cynthia@cs.duke.edu"), person("Alexander", "Volfovsky", role = c("aut"), email = "alexander.volfovsky@duke.edu"), person("Sudeepa", "Roy", role = c("aut"), email = "sudeepa@cs.duke.edu"), person("Tianyu", "Wang", role = c("ctb"), email = "tianyu@cs.duke.edu"))
Description: The 'FLAME' (Fast Large-scale Almost Matching Exactly) package implements the matching algorithm in Roy, Rudin, Volfovsky, and Wang (2017) <arXiv:1707.06315>. 'FLAME' performs matching of treatment and control units in the potential outcomes framework for large categorical datasets. 'FLAME' creates matches that include as many covariates as possible, and sequentially drops covariates that are less useful based on a match quality measure. Match quality combines two important elements – it considers predictive power from machine learning on a hold out training set, and a balancing factor to ensure that it does not remove a covariate that would ruin overlap between treatment and control groups. Currently the 'FLAME' package applies to categorical data, and provides two approaches for implementation - bit vectors and database management systems (e.g., 'PostgreSQL', 'SQLite'). For data that has been adequately processed and fits in memory, bit vectors should be applied. For extremely large data that does not fit in memory, database systems should be applied.
Maintainer: Chia-Rui (Jerry) Chang <chiarui424@gmail.com>
URL: https://chiarui424.github.io/FLAME/
BugReports: https://github.com/chiarui424/FLAME/issues
Depends: R (>= 3.3)
Imports: reticulate (>= 1.9), graphics, stats, latticeExtra, dplyr, RPostgreSQL, RSQLite, gmp, lattice, rlang
Suggests: knitr, rmarkdown, ggplot2, ggpubr, e1071
License: GPL-3
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-09 19:57:40 UTC; Jerry
Author: Chia-Rui (Jerry) Chang [aut, cre], Cynthia Rudin [aut], Alexander Volfovsky [aut], Sudeepa Roy [aut], Tianyu Wang [ctb]
Repository: CRAN
Date/Publication: 2018-12-17 23:40:08 UTC

More information about FLAME at CRAN
Permanent link

New package dbparser with initial version 1.0.0
Package: dbparser
Title: 'DrugBank' Database XML Parser
Version: 1.0.0
Authors@R: c( person("Mohammed", "Ali", email = "moh_fcis@yahoo.com", role = c("aut", "cre")), person("Ali", "Ezzat", email = "ali_ezzat85@yahoo.com", role = "aut"))
Description: This tool is for parsing the 'DrugBank' XML database <http://drugbank.ca/>. The parsed data are then returned in a proper 'R' dataframe with the ability to save them in a given database.
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
Imports: DBI, dplyr, ggplot2, odbc, purrr, tibble, XML
RoxygenNote: 6.1.0
Suggests: knitr, rmarkdown, testthat
VignetteBuilder: knitr
URL: https://github.com/Dainanahan/dbparser
BugReports: https://github.com/Dainanahan/dbparser/issues
NeedsCompilation: no
Packaged: 2018-12-09 16:45:21 UTC; Mohammed
Author: Mohammed Ali [aut, cre], Ali Ezzat [aut]
Maintainer: Mohammed Ali <moh_fcis@yahoo.com>
Repository: CRAN
Date/Publication: 2018-12-17 23:40:03 UTC

More information about dbparser at CRAN
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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>

Diff between spelling versions 1.2 dated 2018-07-09 and 2.0 dated 2018-12-17

 DESCRIPTION                |   10 +++++-----
 MD5                        |   23 ++++++++++++-----------
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 13 files changed, 113 insertions(+), 35 deletions(-)

More information about spelling at CRAN
Permanent link

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>

Diff between Eagle versions 1.1.0 dated 2018-08-22 and 1.2.0 dated 2018-12-17

 DESCRIPTION                             |    6 
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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>

Diff between kohonen versions 3.0.7 dated 2018-11-01 and 3.0.8 dated 2018-12-17

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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>

Diff between pinyin versions 1.1.4 dated 2018-10-17 and 1.1.5 dated 2018-12-17

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Package RSurveillance (with last version 0.2.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2016-10-03 0.2.0
2014-12-08 0.1.0

Permanent link

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>

Diff between arulesCBA versions 1.1.3-1 dated 2018-04-23 and 1.1.4 dated 2018-12-16

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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>

Diff between convexjlr versions 0.7.0 dated 2018-04-28 and 0.8.1 dated 2018-12-16

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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>

Diff between bookdownplus versions 1.5.2 dated 2018-10-16 and 1.5.4 dated 2018-12-16

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New package geohashTools with initial version 0.2.0
Package: geohashTools
Version: 0.2.0
Title: Tools for Working with Geohashes
Author: Michael Chirico, Hiroaki Kawai
Maintainer: Michael Chirico <MichaelChirico4@gmail.com>
Depends: R (>= 3.0.0)
Description: Tools for working with Gustavo Niemeyer's geohash coordinate system, ported to R from Hiroaki Kawai's 'Python' implementation and embellished to sit naturally in the R ecosystem.
URL: https://github.com/MichaelChirico/geohashTools
License: MIT + file LICENSE
Imports: Rcpp (>= 1.0.0)
Suggests: sf, sp, testthat, mockery
LinkingTo: Rcpp
NeedsCompilation: yes
Packaged: 2018-12-07 12:22:49 UTC; michael.chirico
Repository: CRAN
Date/Publication: 2018-12-16 16:10:03 UTC

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New package CornerstoneR with initial version 1.0.0
Package: CornerstoneR
Version: 1.0.0
Title: Collection for 'CornerstoneR' Interface
Description: Collection of scripts for interface between 'Cornerstone' and 'R'. 'Cornerstone' (<https://www.camline.com/>) as a software for engineering analytics supports an interface to 'R'. The scripts are designed to support an easy usage of this interface.
Authors@R: c( person("Dirk", "Surmann", NULL, "dirk.surmann@versuchsplanung.de" , role = c("aut", "cre"), comment = c(ORCID = "0000-0003-0873-137X")) )
URL: https://gitlab.com/camLine/CornerstoneR
BugReports: https://gitlab.com/camLine/CornerstoneR/issues
License: GPL-3
Encoding: UTF-8
Depends: R (>= 3.2.1)
Imports: checkmate (>= 1.5) , data.table (>= 1.10) , ranger , vcd
Suggests: knitr , rmarkdown , testthat
ByteCompile: yes
LazyData: yes
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-08 12:08:10 UTC; Dirk
Author: Dirk Surmann [aut, cre] (<https://orcid.org/0000-0003-0873-137X>)
Maintainer: Dirk Surmann <dirk.surmann@versuchsplanung.de>
Repository: CRAN
Date/Publication: 2018-12-16 16:50:02 UTC

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New package tinter with initial version 0.0.1
Package: tinter
Title: Generate a Monochromatic Palette
Version: 0.0.1
Authors@R: c( person("Sebastian", "Dalgarno", role = c("aut", "cre"), email = "seb@poissonconsulting.ca"), person("Joe", "Thorley", role = "ctb", email = "joe@poissonconsulting.ca", comment = c(ORCID = "0000-0002-7683-4592")))
Description: Generate a palette of tints, shades or both from a single colour.
URL: https://github.com/poissonconsulting/tinter
BugReports: https://github.com/poissonconsulting/tinter/issues
Imports: checkr, grDevices
Suggests: graphics, covr, testthat
License: MIT + file LICENSE
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
Language: en-US
NeedsCompilation: no
Packaged: 2018-12-06 00:06:41 UTC; sebastiandalgarno
Author: Sebastian Dalgarno [aut, cre], Joe Thorley [ctb] (<https://orcid.org/0000-0002-7683-4592>)
Maintainer: Sebastian Dalgarno <seb@poissonconsulting.ca>
Repository: CRAN
Date/Publication: 2018-12-16 15:10:03 UTC

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New package lmreg with initial version 1.0
Package: lmreg
Type: Package
Title: Data and Functions Used in Linear Models and Regression with R: An Integrated Approach
Version: 1.0
Date: 2018-11-13
Author: Debasis Sengupta <shairiksengupta@gmail.com>, S. Rao Jammalamadaka <rao@gmail.com>, Jinwen Qiu <qjwsnow_ctw@hotmail.com>
Maintainer: Jinwen Qiu <qjwsnow_ctw@hotmail.com>
Description: Data files and a few functions used in the book 'Linear Models and Regression with R: An Integrated Approach' by Debasis Sengupta and Sreenivas Rao Jammalamadaka (2019).
License: GPL (>= 2)
NeedsCompilation: no
Repository: CRAN
Depends: MASS
Packaged: 2018-12-06 20:28:25 UTC; william
Date/Publication: 2018-12-16 16:00:02 UTC

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New package mined with initial version 1.0-1
Package: mined
Type: Package
Title: Minimum Energy Designs
Version: 1.0-1
Date: 2018-11-24
Author: Dianpeng Wang and V. Roshan Joseph
Maintainer: Dianpeng Wang <wdp@bit.edu.cn>
Description: This is a method (MinED) for mining probability distributions using deterministic sampling which is proposed by Joseph, Wang, Gu, Lv, and Tuo (2018). The MinED samples can be used for approximating the target distribution. They can be generated from a density function that is known only up to a proportionality constant and thus, it might find applications in Bayesian computation. Moreover, the MinED samples are generated with much fewer evaluations of the density function compared to random sampling-based methods such as MCMC and therefore, this method will be especially useful when the unnormalized posterior is expensive or time consuming to evaluate.
License: LGPL-2.1
Imports: Rcpp (>= 0.12.17)
LinkingTo: Rcpp, RcppEigen
NeedsCompilation: yes
Packaged: 2018-12-05 08:22:40 UTC; Administrator
Repository: CRAN
Date/Publication: 2018-12-16 14:40:02 UTC

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New package epiGWAS with initial version 1.0.0
Package: epiGWAS
Title: Robust Methods for Epistasis Detection
Version: 1.0.0
Authors@R: c(person("Lotfi", "Slim", email = "lotfi.slim@mines-paristech.fr", role = c("aut", "cre")), person("Clément", "Chatelain", email = "clement.chatelain@sanofi.com", role = "ctb"), person("Chloé-Agathe", "Azencott", email = "chloe-agathe.azencott@mines-paristech.fr", role ="ctb"), person("Jean-Philippe", "Vert", email = "jpvert@google.com", role ="ctb"))
Description: Functions to perform robust epistasis detection in genome-wide association studies, as described in Slim et al. (2018) <doi:10.1101/442749>. The implemented methods identify pairwise interactions between a particular target variant and the rest of the genotype, using a propensity score approach. The propensity score models the linkage disequilibrium between the target and the rest of the genotype. All methods are penalized regression approaches, which differently incorporate the propensity score to only recover the synergistic effects between the target and the genotype.
Depends: R (>= 3.4.0)
Imports: matrixStats, DescTools, glmnet, SNPknock
Suggests: foreach, iterators, precrec, parallel, doParallel, bigmemory, biglasso, testthat, knitr, rmarkdown, kableExtra
License: GPL (>= 2)
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.1.1
VignetteBuilder: knitr
NeedsCompilation: no
Packaged: 2018-12-04 20:00:21 UTC; lotfislim
Author: Lotfi Slim [aut, cre], Clément Chatelain [ctb], Chloé-Agathe Azencott [ctb], Jean-Philippe Vert [ctb]
Maintainer: Lotfi Slim <lotfi.slim@mines-paristech.fr>
Repository: CRAN
Date/Publication: 2018-12-16 14:10:03 UTC

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New package cliapp with initial version 0.1.0
Package: cliapp
Title: Create Rich Command Line Applications
Version: 0.1.0
Author: Gábor Csárdi
Maintainer: Gábor Csárdi <csardi.gabor@gmail.com>
Description: Create rich command line applications, with colors, headings, lists, alerts, progress bars, etc. It uses CSS for custom themes.
License: MIT + file LICENSE
LazyData: true
URL: https://github.com/r-lib/cliapp#readme
BugReports: https://github.com/r-lib/cliapp/issues
RoxygenNote: 6.1.1
Imports: cli, crayon, fansi, glue (>= 1.3.0), prettycode, progress (>= 1.2.0), R6, selectr, utils, withr, xml2
Suggests: callr, covr, rstudioapi, testthat
Encoding: UTF-8
NeedsCompilation: no
Packaged: 2018-12-05 09:41:39 UTC; gaborcsardi
Repository: CRAN
Date/Publication: 2018-12-16 14:40:05 UTC

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New package bfsl with initial version 0.1.0
Package: bfsl
Title: Best-Fit Straight Line
Version: 0.1.0
Authors@R: person("Patrick", "Sturm", email = "sturm@tofwerk.com", role = c("aut", "cre"))
Description: Provides the solution from York (1968) <doi:10.1016/S0012-821X(68)80059-7> for fitting a straight line to bivariate data with errors in both coordinates. It gives unbiased estimates of the intercept, slope and standard errors of the best-fit straight line to independent points with (possibly correlated) normally distributed errors in both x and y. Other commonly used errors-in-variables methods, such as orthogonal distance regression, geometric mean regression or Deming regression are special cases of York’s solution.
Depends: R (>= 3.5.0)
License: GPL-3
URL: https://github.com/pasturm/bfsl
BugReports: https://github.com/pasturm/bfsl/issues
Encoding: UTF-8
LazyData: true
RoxygenNote: 6.0.1
Suggests: testthat
NeedsCompilation: no
Packaged: 2018-12-05 12:58:44 UTC; pst
Author: Patrick Sturm [aut, cre]
Maintainer: Patrick Sturm <sturm@tofwerk.com>
Repository: CRAN
Date/Publication: 2018-12-16 14:50:03 UTC

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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>

Diff between texteffect versions 0.1 dated 2017-11-27 and 0.2 dated 2018-12-16

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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>

Diff between LadR versions 1.0.4 dated 2018-08-06 and 1.0.5 dated 2018-12-16

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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>

Diff between schoRsch versions 1.4 dated 2017-02-14 and 1.5 dated 2018-12-15

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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>

Diff between foolbox versions 0.1.0 dated 2018-04-27 and 0.1.1 dated 2018-12-15

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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>

Diff between AdvDif4 versions 0.3.18 dated 2018-09-13 and 0.4.18 dated 2018-12-15

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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>

Diff between redist versions 1.3-2 dated 2018-10-17 and 1.3-3 dated 2018-12-15

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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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More information about QuantumOps at CRAN
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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 115 files changed, 1506 insertions(+), 1456 deletions(-)

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>

Diff between hunspell versions 2.9 dated 2017-12-16 and 3.0 dated 2018-12-15

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More information about hunspell at CRAN
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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More information about rscala at CRAN
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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New package bioRad with initial version 0.4.0
Package: bioRad
Title: Biological Analysis and Visualization of Weather Radar Data
Version: 0.4.0
Description: Extract, visualize and summarize aerial movements of birds and insects from weather radar data.
Authors@R: c( person("Adriaan M.", "Dokter", role = c("aut", "cre"), email = "amd427@cornell.edu", comment = c(ORCID = "0000-0001-6573-066X")), person("Peter", "Desmet", role = "aut", email = "peter.desmet@inbo.be", comment = c(ORCID = "0000-0002-8442-8025")), person("Stijn", "Van Hoey", role = "aut", email = "stijn.vanhoey@inbo.be", comment = c(ORCID = "0000-0001-6413-3185")), person("Jurriaan", "Spaaks", role = "ctb", email = "j.spaaks@esciencecenter.nl"), person("Lourens", "Veen", role = "ctb", email = "l.veen@esciencecenter.nl"), person("Liesbeth", "Verlinden", role = "ctb", email = "l.verlinden@uva.nl", comment = c(ORCID = "0000-0003-1744-9325")), person("Hidde", "Leijnse", role = "ctb", email = "hidde.leijnse@knmi.nl", comment = c(ORCID = "0000-0001-7835-4480")) )
License: MIT + file LICENSE
URL: https://github.com/adokter/bioRad, https://adokter.github.io/bioRad
BugReports: https://github.com/adokter/bioRad/issues
biocViews:
Depends: R (>= 2.10)
Imports: curl, fields, ggmap, ggplot2, graphics, methods, raster, rgdal, rhdf5, sp, stats, utils, maptools
Suggests: knitr, testthat
LazyData: true
Encoding: UTF-8
VignetteBuilder: knitr
RoxygenNote: 6.1.1
NeedsCompilation: no
Packaged: 2018-12-14 20:54:42 UTC; amd427
Author: Adriaan M. Dokter [aut, cre] (<https://orcid.org/0000-0001-6573-066X>), Peter Desmet [aut] (<https://orcid.org/0000-0002-8442-8025>), Stijn Van Hoey [aut] (<https://orcid.org/0000-0001-6413-3185>), Jurriaan Spaaks [ctb], Lourens Veen [ctb], Liesbeth Verlinden [ctb] (<https://orcid.org/0000-0003-1744-9325>), Hidde Leijnse [ctb] (<https://orcid.org/0000-0001-7835-4480>)
Maintainer: Adriaan M. Dokter <amd427@cornell.edu>
Repository: CRAN
Date/Publication: 2018-12-14 21:30:04 UTC

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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

 DESCRIPTION                   |    8 
 MD5                           |   29 +-
 R/plot.stslist.surv.R         |    4 
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 R/seqprecarity.R              |   28 ++
 R/seqprecorr.R                |  407 ++++++++++++++++++++----------------------
 R/seqprecstart.R              |   53 +----
 R/seqsplot.R                  |   35 +--
 R/seqsurv.R                   |   13 +
 inst/CITATION                 |    8 
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 16 files changed, 383 insertions(+), 336 deletions(-)

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Permanent link

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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 NAMESPACE                     |    4 ++++
 NEWS.md                       |    5 +++++
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 R/import.R                    |   11 ++++++-----
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 tests/test_capture.output.R   |only
 tests/test_warningCondition.R |only
 17 files changed, 51 insertions(+), 26 deletions(-)

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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

 DESCRIPTION     |   10 +++++-----
 MD5             |   28 ++++++++++++++--------------
 NAMESPACE       |    1 +
 R/RSA.R         |   12 ++++++++++--
 R/demoRSA.R     |   44 +++++++++++++++++++++++---------------------
 R/imports.R     |    2 +-
 R/plot.RSA.R    |    4 ++++
 R/print.RSA.R   |    2 +-
 inst/News.Rd    |   23 +++++++++++++++++++++++
 man/RSA.Rd      |   11 ++++++-----
 man/RSA.ST.Rd   |    4 ++--
 man/aictab.Rd   |    4 ++--
 man/demoRSA.Rd  |   10 +++++-----
 man/movieRSA.Rd |    4 ++--
 man/plotRSA.Rd  |   41 +++++++++++++++++++++--------------------
 15 files changed, 120 insertions(+), 80 deletions(-)

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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

 DESCRIPTION                               |   22 -
 MD5                                       |   21 -
 NAMESPACE                                 |   39 +-
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 man/EstDimIC.Rd                           |   58 +--
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Permanent link

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

 ChangeLog     |    5 +
 DESCRIPTION   |    8 +-
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 R/pgmmEM.R    |  176 ++++++++++++++++++++++++++++------------------------------
 man/pgmm.Rd   |    4 -
 man/pgmmEM.Rd |    4 -
 src/aecm.c    |   49 +++++++++++-----
 7 files changed, 142 insertions(+), 116 deletions(-)

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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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 NEWS.md                    |    4 +
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 R/bd.R                     |   82 +++++++++++++++++-----------------
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 R/wrap_c.R                 |   50 ++++++++++-----------
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 man/bd.Rd                  |    8 +--
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 tests/testthat/test_bcov.R |   20 ++++----
 tests/testthat/test_bd.R   |   26 +++++------
 17 files changed, 266 insertions(+), 251 deletions(-)

More information about Ball at CRAN
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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

 DESCRIPTION                                      |   12 ++++++------
 MD5                                              |   20 ++++++++++----------
 NAMESPACE                                        |    2 +-
 R/RcppExports.R                                  |    2 +-
 R/starts_uni_estimate.R                          |    2 +-
 R/starts_uni_estimate_variance_proportions_pml.R |   14 +++-----------
 build/partial.rdb                                |binary
 inst/NEWS                                        |    8 ++++++++
 man/data.starts.Rd                               |    8 ++++----
 man/starts_uni.Rd                                |    6 +++---
 src/RcppExports.cpp                              |    2 +-
 11 files changed, 38 insertions(+), 38 deletions(-)

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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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 pomp-1.19/pomp/NAMESPACE                     |    7 
 pomp-1.19/pomp/R/aaa.R                       |    8 
 pomp-1.19/pomp/R/abc.R                       |  533 +++++++++----------
 pomp-1.19/pomp/R/bsmc.R                      |    2 
 pomp-1.19/pomp/R/builder.R                   |  477 ++++++++---------
 pomp-1.19/pomp/R/dprocess_pomp.R             |    6 
 pomp-1.19/pomp/R/generics.R                  |    3 
 pomp-1.19/pomp/R/load.R                      |    4 
 pomp-1.19/pomp/R/mif.R                       |    3 
 pomp-1.19/pomp/R/mif2.R                      |  563 ++++++++++----------
 pomp-1.19/pomp/R/nlf_objfun.R                |  114 ++--
 pomp-1.19/pomp/R/pfilter.R                   |  145 ++---
 pomp-1.19/pomp/R/plugins.R                   |  340 ++----------
 pomp-1.19/pomp/R/pmcmc.R                     |  580 ++++++++++-----------
 pomp-1.19/pomp/R/pomp.R                      |  742 +++++++++++----------------
 pomp-1.19/pomp/R/pomp_class.R                |  204 +++----
 pomp-1.19/pomp/R/pomp_fun.R                  |  265 ++++-----
 pomp-1.19/pomp/R/pomp_methods.R              |  159 +++--
 pomp-1.19/pomp/R/probe.R                     |    3 
 pomp-1.19/pomp/R/probe_match.R               |    3 
 pomp-1.19/pomp/R/rprocess_pomp.R             |    4 
 pomp-1.19/pomp/R/sannbox.R                   |  212 ++++---
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 pomp-1.19/pomp/demo/logistic.R               |   55 --
 pomp-1.19/pomp/demo/rw2.R                    |   67 +-
 pomp-1.19/pomp/inst/NEWS                     |   76 ++
 pomp-1.19/pomp/inst/NEWS.Rd                  |   33 +
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 pomp-1.19/pomp/inst/examples/blowflies.R     |  149 +++--
 pomp-1.19/pomp/inst/examples/euler.sir.R     |  188 +++++-
 pomp-1.19/pomp/inst/examples/gillespie.sir.R |  136 +++-
 pomp-1.19/pomp/inst/examples/ou2.R           |   46 -
 pomp-1.19/pomp/inst/examples/ricker.R        |   58 +-
 pomp-1.19/pomp/inst/examples/rw2.R           |   56 --
 pomp-1.19/pomp/inst/include/pomp.h           |   21 
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 pomp-1.19/pomp/man/traj_match.Rd             |    2 
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 pomp-1.19/pomp/src/euler.c                   |  215 -------
 pomp-1.19/pomp/src/init.c                    |   16 
 pomp-1.19/pomp/src/lookup_table.c            |    9 
 pomp-1.19/pomp/src/pfilter.c                 |   79 +-
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 pomp-1.19/pomp/src/pomp_fun.c                |   17 
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 pomp-1.19/pomp/src/probe.c                   |    9 
 pomp-1.19/pomp/src/rprocess.c                |   92 +--
 pomp-1.19/pomp/src/skeleton.c                |   26 
 pomp-1.19/pomp/src/trajectory.c              |   24 
 pomp-1.19/pomp/src/userdata.c                |    4 
 68 files changed, 3286 insertions(+), 3494 deletions(-)

More information about pomp at CRAN
Permanent link

New package norm2 with initial version 2.0.2
Package: norm2
Type: Package
Title: Analysis of Incomplete Multivariate Data under a Normal Model
Version: 2.0.2
Date: 2018-12-12
Author: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Maintainer: Joseph L. Schafer <Joseph.L.Schafer@census.gov>
Description: Functions for parameter estimation, Bayesian posterior simulation and multiple imputation from incomplete multivariate data under a normal model.
Depends: R (>= 3.1.0)
Imports: stats
License: GPL-3
LazyLoad: yes
NeedsCompilation: yes
Packaged: 2018-12-13 11:25:36 UTC; schaf310
Repository: CRAN
Date/Publication: 2018-12-14 00:00:03 UTC

More information about norm2 at CRAN
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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

 DESCRIPTION            |    6 +++---
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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>

Diff between hBayesDM versions 0.6.0 dated 2018-09-11 and 0.7.0 dated 2018-12-13

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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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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>

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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>

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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>

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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>

Diff between glmc versions 0.2-4 dated 2012-12-04 and 0.3-1 dated 2018-12-12

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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 irteQ (with last version 1.0.0) was removed from CRAN

Previous versions (as known to CRANberries) which should be available via the Archive link are:

2018-11-19 1.0.0

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