Title: Presentation-Ready Data Summary and Analytic Result Tables
Description: Creates presentation-ready tables summarizing data
sets, regression models, and more. The code to create the tables is
concise and highly customizable. Data frames can be summarized with
any function, e.g. mean(), median(), even user-written functions.
Regression models are summarized and include the reference rows for
categorical variables. Common regression models, such as logistic
regression and Cox proportional hazards regression, are automatically
identified and the tables are pre-filled with appropriate column
headers. The package is enhanced when the 'gt' package is installed.
Use this code to install: 'remotes::install_github("rstudio/gt", ref =
gtsummary::gt_sha)'.
Author: Daniel D. Sjoberg [aut, cre] (<https://orcid.org/0000-0003-0862-2018>),
Margie Hannum [aut] (<https://orcid.org/0000-0002-2953-0449>),
Karissa Whiting [aut] (<https://orcid.org/0000-0002-4683-1868>),
Emily C. Zabor [aut] (<https://orcid.org/0000-0002-1402-4498>),
Michael Curry [ctb] (<https://orcid.org/0000-0002-0261-4044>),
Esther Drill [ctb] (<https://orcid.org/0000-0002-3315-4538>),
Jessica Flynn [ctb] (<https://orcid.org/0000-0001-8310-6684>),
Stephanie Lobaugh [ctb]
Maintainer: Daniel D. Sjoberg <danield.sjoberg@gmail.com>
Diff between gtsummary versions 1.2.4 dated 2019-12-16 and 1.2.5 dated 2020-02-11
gtsummary-1.2.4/gtsummary/man/add_p_.Rd |only gtsummary-1.2.4/gtsummary/man/figures/gtsummary-HexSticker.jpg |only gtsummary-1.2.4/gtsummary/man/figures/gtsummary-HexSticker.pdf |only gtsummary-1.2.4/gtsummary/man/figures/gtsummary-HexSticker.png |only gtsummary-1.2.4/gtsummary/man/tbl_summary_.Rd |only gtsummary-1.2.4/gtsummary/tests/testthat/test-utils-calculate_summary_stat.R |only gtsummary-1.2.5/gtsummary/DESCRIPTION | 36 gtsummary-1.2.5/gtsummary/MD5 | 335 gtsummary-1.2.5/gtsummary/NAMESPACE | 35 gtsummary-1.2.5/gtsummary/NEWS.md | 79 gtsummary-1.2.5/gtsummary/R/add_global_p.R | 76 gtsummary-1.2.5/gtsummary/R/add_n.R | 5 gtsummary-1.2.5/gtsummary/R/add_nevent.R | 20 gtsummary-1.2.5/gtsummary/R/add_overall.R | 5 gtsummary-1.2.5/gtsummary/R/add_p.R | 83 gtsummary-1.2.5/gtsummary/R/add_q.R | 18 gtsummary-1.2.5/gtsummary/R/add_stat_label.R | 3 gtsummary-1.2.5/gtsummary/R/as_gt.R | 69 gtsummary-1.2.5/gtsummary/R/as_kable.R | 82 gtsummary-1.2.5/gtsummary/R/as_tibble.R | 59 gtsummary-1.2.5/gtsummary/R/bold_italicise_labels_levels.R | 19 gtsummary-1.2.5/gtsummary/R/bold_p.R | 8 gtsummary-1.2.5/gtsummary/R/combine_terms.R |only gtsummary-1.2.5/gtsummary/R/data.R | 16 gtsummary-1.2.5/gtsummary/R/deprecated.R | 53 gtsummary-1.2.5/gtsummary/R/gtsummary-package.R | 15 gtsummary-1.2.5/gtsummary/R/inline_text.R | 175 gtsummary-1.2.5/gtsummary/R/modify_header.R | 2 gtsummary-1.2.5/gtsummary/R/print.R | 59 gtsummary-1.2.5/gtsummary/R/reexport.R | 25 gtsummary-1.2.5/gtsummary/R/sort_p.R | 6 gtsummary-1.2.5/gtsummary/R/style_percent.R | 2 gtsummary-1.2.5/gtsummary/R/style_pvalue.R | 2 gtsummary-1.2.5/gtsummary/R/style_ratio.R | 2 gtsummary-1.2.5/gtsummary/R/style_sigfig.R | 2 gtsummary-1.2.5/gtsummary/R/tbl_merge.R | 55 gtsummary-1.2.5/gtsummary/R/tbl_regression.R | 123 gtsummary-1.2.5/gtsummary/R/tbl_stack.R | 54 gtsummary-1.2.5/gtsummary/R/tbl_summary.R | 197 gtsummary-1.2.5/gtsummary/R/tbl_survival.R | 22 gtsummary-1.2.5/gtsummary/R/tbl_uvregression.R | 349 gtsummary-1.2.5/gtsummary/R/tidy_vetted.R |only gtsummary-1.2.5/gtsummary/R/tidyselect_to_list.R | 216 gtsummary-1.2.5/gtsummary/R/utils-add_p.R | 20 gtsummary-1.2.5/gtsummary/R/utils-table_headers.R | 61 gtsummary-1.2.5/gtsummary/R/utils-tbl_regression.R | 153 gtsummary-1.2.5/gtsummary/R/utils-tbl_summary.R | 1170 gtsummary-1.2.5/gtsummary/README.md | 168 gtsummary-1.2.5/gtsummary/build/gtsummary.pdf |15323 ++++------ gtsummary-1.2.5/gtsummary/build/vignette.rds |binary gtsummary-1.2.5/gtsummary/data/gt_sha.rda |only gtsummary-1.2.5/gtsummary/inst/WORDLIST | 5 gtsummary-1.2.5/gtsummary/inst/doc/gallery.R | 63 gtsummary-1.2.5/gtsummary/inst/doc/gallery.Rmd | 75 gtsummary-1.2.5/gtsummary/inst/doc/gallery.html | 1793 - gtsummary-1.2.5/gtsummary/inst/doc/global_options.R | 7 gtsummary-1.2.5/gtsummary/inst/doc/global_options.Rmd | 11 gtsummary-1.2.5/gtsummary/inst/doc/global_options.html | 124 gtsummary-1.2.5/gtsummary/inst/doc/gtsummary_definition.R |only gtsummary-1.2.5/gtsummary/inst/doc/gtsummary_definition.Rmd |only gtsummary-1.2.5/gtsummary/inst/doc/gtsummary_definition.html |only gtsummary-1.2.5/gtsummary/inst/doc/inline_text.R |only gtsummary-1.2.5/gtsummary/inst/doc/inline_text.Rmd |only gtsummary-1.2.5/gtsummary/inst/doc/inline_text.html |only gtsummary-1.2.5/gtsummary/inst/doc/tbl_regression.R | 17 gtsummary-1.2.5/gtsummary/inst/doc/tbl_regression.Rmd | 160 gtsummary-1.2.5/gtsummary/inst/doc/tbl_regression.html | 1074 gtsummary-1.2.5/gtsummary/inst/doc/tbl_summary.R | 47 gtsummary-1.2.5/gtsummary/inst/doc/tbl_summary.Rmd | 169 gtsummary-1.2.5/gtsummary/inst/doc/tbl_summary.html | 1247 gtsummary-1.2.5/gtsummary/man/add_global_p.Rd | 4 gtsummary-1.2.5/gtsummary/man/add_global_p.tbl_regression.Rd | 22 gtsummary-1.2.5/gtsummary/man/add_global_p.tbl_uvregression.Rd | 3 gtsummary-1.2.5/gtsummary/man/add_n.Rd | 3 gtsummary-1.2.5/gtsummary/man/add_nevent.tbl_regression.Rd | 4 gtsummary-1.2.5/gtsummary/man/add_nevent.tbl_uvregression.Rd | 3 gtsummary-1.2.5/gtsummary/man/add_overall.Rd | 3 gtsummary-1.2.5/gtsummary/man/add_p.Rd | 262 gtsummary-1.2.5/gtsummary/man/add_q.tbl_summary.Rd | 5 gtsummary-1.2.5/gtsummary/man/add_q.tbl_uvregression.Rd | 5 gtsummary-1.2.5/gtsummary/man/add_stat_label.Rd | 3 gtsummary-1.2.5/gtsummary/man/as_gt.Rd | 20 gtsummary-1.2.5/gtsummary/man/as_kable.Rd | 30 gtsummary-1.2.5/gtsummary/man/as_tibbleS3.Rd | 110 gtsummary-1.2.5/gtsummary/man/bold_italicize_labels_levels.Rd | 4 gtsummary-1.2.5/gtsummary/man/bold_p.tbl_regression.Rd | 1 gtsummary-1.2.5/gtsummary/man/bold_p.tbl_stack.Rd | 1 gtsummary-1.2.5/gtsummary/man/bold_p.tbl_summary.Rd | 3 gtsummary-1.2.5/gtsummary/man/bold_p.tbl_uvregression.Rd | 3 gtsummary-1.2.5/gtsummary/man/combine_terms.Rd |only gtsummary-1.2.5/gtsummary/man/deprecated.Rd | 20 gtsummary-1.2.5/gtsummary/man/figures/README-tbl_merge_ex1-1.png |only gtsummary-1.2.5/gtsummary/man/figures/README-tbl_merge_ex1.png |only gtsummary-1.2.5/gtsummary/man/figures/README-tbl_regression_print-1.png |binary gtsummary-1.2.5/gtsummary/man/figures/README-tbl_regression_printa-1.png |only gtsummary-1.2.5/gtsummary/man/figures/README-tbl_summary_print-1.png |binary gtsummary-1.2.5/gtsummary/man/figures/README-tbl_summary_print_extra-1.png |only gtsummary-1.2.5/gtsummary/man/figures/README-tbl_summary_print_simple-1.png |only gtsummary-1.2.5/gtsummary/man/figures/add_p_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/add_p_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/as_gt_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/bold_p_stack_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/combine_terms_ex1.png |only gtsummary-1.2.5/gtsummary/man/figures/combine_terms_ex2.png |only gtsummary-1.2.5/gtsummary/man/figures/combine_terms_ex3.png |only gtsummary-1.2.5/gtsummary/man/figures/inline_text_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/modify_anova_ex1.png |only gtsummary-1.2.5/gtsummary/man/figures/tbl_bold_ital_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_col_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_col_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_lm_bold_p_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_lm_global_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_lm_sort_p_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_merge_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_merge_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_mvregression_demo.gif |only gtsummary-1.2.5/gtsummary/man/figures/tbl_n_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_nostrata_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_overall_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_reg_nevent_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_regression_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_regression_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_regression_ex3.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_stack_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_stack_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_stat_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_strata_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_sum_bold_p_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_sum_q_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_sum_sort_p_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_summary_demo1.gif |only gtsummary-1.2.5/gtsummary/man/figures/tbl_summary_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_summary_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_summary_ex3.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_uv_ex1.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_uv_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_uv_global_ex2.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_uv_nevent_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_uvglm_bold_p_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_uvglm_sort_p_ex.png |binary gtsummary-1.2.5/gtsummary/man/figures/tbl_uvr_q_ex.png |binary gtsummary-1.2.5/gtsummary/man/gt_sha.Rd |only gtsummary-1.2.5/gtsummary/man/gtsummary-package.Rd | 4 gtsummary-1.2.5/gtsummary/man/inline_text.tbl_regression.Rd | 9 gtsummary-1.2.5/gtsummary/man/inline_text.tbl_summary.Rd | 145 gtsummary-1.2.5/gtsummary/man/inline_text.tbl_survival.Rd | 170 gtsummary-1.2.5/gtsummary/man/inline_text.tbl_uvregression.Rd | 11 gtsummary-1.2.5/gtsummary/man/modify_header.Rd | 1 gtsummary-1.2.5/gtsummary/man/print_gtsummary.Rd | 40 gtsummary-1.2.5/gtsummary/man/reexports.Rd | 8 gtsummary-1.2.5/gtsummary/man/sort_p.tbl_regression.Rd | 1 gtsummary-1.2.5/gtsummary/man/sort_p.tbl_summary.Rd | 3 gtsummary-1.2.5/gtsummary/man/sort_p.tbl_uvregression.Rd | 3 gtsummary-1.2.5/gtsummary/man/style_percent.Rd | 9 gtsummary-1.2.5/gtsummary/man/style_pvalue.Rd | 9 gtsummary-1.2.5/gtsummary/man/style_ratio.Rd | 6 gtsummary-1.2.5/gtsummary/man/style_sigfig.Rd | 7 gtsummary-1.2.5/gtsummary/man/tbl_merge.Rd | 11 gtsummary-1.2.5/gtsummary/man/tbl_regression.Rd | 312 gtsummary-1.2.5/gtsummary/man/tbl_stack.Rd | 9 gtsummary-1.2.5/gtsummary/man/tbl_summary.Rd | 409 gtsummary-1.2.5/gtsummary/man/tbl_survival.Rd | 6 gtsummary-1.2.5/gtsummary/man/tbl_survival.survfit.Rd | 254 gtsummary-1.2.5/gtsummary/man/tbl_uvregression.Rd | 404 gtsummary-1.2.5/gtsummary/man/tidy_vetted.Rd | 89 gtsummary-1.2.5/gtsummary/man/trial.Rd | 52 gtsummary-1.2.5/gtsummary/tests/testthat.R | 1 gtsummary-1.2.5/gtsummary/tests/testthat/test-add_n.R | 6 gtsummary-1.2.5/gtsummary/tests/testthat/test-add_p.R | 16 gtsummary-1.2.5/gtsummary/tests/testthat/test-combine_terms.R |only gtsummary-1.2.5/gtsummary/tests/testthat/test-inline_text.R | 19 gtsummary-1.2.5/gtsummary/tests/testthat/test-select_helpers.R | 87 gtsummary-1.2.5/gtsummary/tests/testthat/test-sort_p.R | 4 gtsummary-1.2.5/gtsummary/tests/testthat/test-tbl_regression.R | 11 gtsummary-1.2.5/gtsummary/tests/testthat/test-tbl_stack.R | 6 gtsummary-1.2.5/gtsummary/tests/testthat/test-tbl_summary.R | 140 gtsummary-1.2.5/gtsummary/tests/testthat/test-tbl_summary_input_checks.R | 8 gtsummary-1.2.5/gtsummary/tests/testthat/test-tbl_uvregression.R | 81 gtsummary-1.2.5/gtsummary/vignettes/gallery.Rmd | 75 gtsummary-1.2.5/gtsummary/vignettes/global_options.Rmd | 11 gtsummary-1.2.5/gtsummary/vignettes/gtsummary_definition.Rmd |only gtsummary-1.2.5/gtsummary/vignettes/inline_text.Rmd |only gtsummary-1.2.5/gtsummary/vignettes/tbl_regression.Rmd | 160 gtsummary-1.2.5/gtsummary/vignettes/tbl_summary.Rmd | 169 184 files changed, 13712 insertions(+), 13557 deletions(-)
Title: Formula Interface to the Grammar of Graphics
Description: Provides a formula interface to 'ggplot2' graphics.
Author: Daniel Kaplan [aut],
Randall Pruim [aut, cre]
Maintainer: Randall Pruim <rpruim@calvin.edu>
Diff between ggformula versions 0.9.2 dated 2019-09-05 and 0.9.3 dated 2020-02-11
DESCRIPTION | 11 MD5 | 166 ++--- NAMESPACE | 7 NEWS.md | 6 R/gf_dist.R | 473 ++++++++-------- R/gf_functions.R | 23 R/layer_factory.R | 17 R/reexports.R | 10 build/vignette.rds |binary inst/doc/ggformula-blog.R | 24 inst/doc/ggformula-blog.html | 167 ++--- inst/doc/ggformula.R | 89 +-- inst/doc/ggformula.Rmd | 15 inst/doc/ggformula.html | 466 ++++++++------- inst/doc/learn-more.R | 2 inst/doc/learn-more.html | 17 inst/tutorials/introduction/Plotting_with_formulas.html | 8 man/geom_lm.Rd | 54 + man/geom_spline.Rd | 52 + man/gf_area.Rd | 33 - man/gf_ash.Rd | 58 + man/gf_aux.Rd | 4 man/gf_bar.Rd | 259 +++++++- man/gf_barh.Rd | 30 - man/gf_bin2d.Rd | 29 man/gf_blank.Rd | 48 + man/gf_boxplot.Rd | 46 + man/gf_boxploth.Rd | 42 + man/gf_col.Rd | 29 man/gf_contour.Rd | 28 man/gf_count.Rd | 32 - man/gf_crossbar.Rd | 64 +- man/gf_curve.Rd | 38 + man/gf_density.Rd | 71 +- man/gf_density_2d.Rd | 78 ++ man/gf_dist.Rd | 10 man/gf_dotplot.Rd | 39 + man/gf_ecdf.Rd | 31 - man/gf_ellipse.Rd | 29 man/gf_errorbar.Rd | 32 - man/gf_errorbarh.Rd | 34 - man/gf_fitdistr.Rd | 31 - man/gf_freqpoly.Rd | 36 - man/gf_function2d.Rd | 102 ++- man/gf_hex.Rd | 34 - man/gf_histogram.Rd | 134 +++- man/gf_jitter.Rd | 32 - man/gf_line.Rd | 66 +- man/gf_linerange.Rd | 159 ++++- man/gf_lines.Rd | 81 ++ man/gf_point.Rd | 30 - man/gf_polygon.Rd | 30 - man/gf_qq.Rd | 88 ++ man/gf_quantile.Rd | 43 + man/gf_raster.Rd | 33 - man/gf_rect.Rd | 29 man/gf_ribbon.Rd | 27 man/gf_rug.Rd | 97 ++- man/gf_segment.Rd | 34 - man/gf_sf.Rd | 33 - man/gf_sina.Rd |only man/gf_smooth.Rd | 60 +- man/gf_spline.Rd | 32 - man/gf_spoke.Rd | 34 - man/gf_step.Rd | 33 - man/gf_text.Rd | 87 ++ man/gf_tile.Rd | 29 man/gf_violin.Rd | 82 ++ man/ggformula-ggproto.Rd | 8 man/layer_factory.Rd | 18 man/reexports.Rd | 7 man/stat_fitdistr.Rd | 15 man/stat_qqline.Rd | 16 tests/figs/deps.txt | 2 tests/figs/layer-factory/gf-fun2d1.svg | 242 ++++---- tests/figs/layer-factory/gf-fun2d3.svg | 232 +++---- tests/figs/layer-factory/gf-fun2d4.svg | 250 ++++---- tests/figs/layer-factory/gf-linerange1.svg | 162 ++--- tests/figs/layer-factory/gf-pointrange1.svg | 2 tests/figs/layer-factory/gf-raster1.svg | 2 tests/figs/layer-factory/gf-sina.svg |only tests/figs/layer-factory/gf-sina2.svg |only tests/figs/layer-factory/gf-sina3.svg |only tests/figs/layer-factory/gf-tile1.svg | 214 +++---- tests/testthat/test-layer-factory.R | 21 vignettes/ggformula.Rmd | 15 86 files changed, 3540 insertions(+), 1813 deletions(-)
Title: A Graphical Interface to Perform STOCSY Analyses on NMR Data
Description: Launches a 'shiny' based application for Nuclear Magnetic Resonance (NMR) data importation and Statistical TOtal Correlation SpectroscopY (STOCSY) analyses in a full interactive approach. The theoretical background and applications of STOCSY method could be found at Cloarec, O., Dumas, M. E., Craig, A., Barton, R. H., Trygg, J., Hudson, J., Blancher, C., Gauguier, D., Lindon, J. C., Holmes, E. & Nicholson, J. (2005) <doi:10.1021/ac048630x>.
Author: Luiz Henrique Keng Queiroz Junior[aut,cre], Vitor Mendes de Oliveira [aut]
Maintainer: Luiz Henrique Keng Queiroz Junior <keng@ufg.br>
Diff between iSTATS versions 1.1.0 dated 2019-11-27 and 1.2 dated 2020-02-11
DESCRIPTION | 12 MD5 | 13 data/datalist | 6 inst/app/home_ui.R | 6 inst/app/select_signals_server.R | 1436 ++++++++++++++++++++------------------- inst/app/select_signals_ui.R | 348 ++++----- inst/app/stocsy_is_ui.R | 2 inst/app/www/fluxogram.png |only 8 files changed, 954 insertions(+), 869 deletions(-)
Title: Deterministic Blockmodeling of Signed, One-Mode and Two-Mode
Networks
Description: It contains functions to apply blockmodeling of signed (positive and negative weights are assigned to the links), one-mode and valued one-mode and two-mode (two sets of nodes are considered, e.g. employees and organizations) networks (Brusco et al. (2019) <doi:10.1111/bmsp.12192>).
Author: Michael Brusco [aut],
Aleš Žiberna [cre],
Marjan Cugmas [ctb],
Patrick Doreian [ctb],
Doug Steinley [ctb]
Maintainer: Aleš Žiberna <ales.ziberna@fdv.uni-lj.si>
Diff between dBlockmodeling versions 0.1.1 dated 2019-12-16 and 0.2.0 dated 2020-02-11
DESCRIPTION | 12 +++++++----- MD5 | 11 ++++++++--- NAMESPACE | 1 + R/omkm.R |only data/notesBorrowing.RData |only man/notesBorrowing.Rd |only man/omkm.Rd |only src/OMKM.f |only src/init.c | 2 ++ 9 files changed, 18 insertions(+), 8 deletions(-)
More information about dBlockmodeling at CRAN
Permanent link
Title: Weighting for Covariate Balance in Observational Studies
Description: Generates weights to form equivalent groups in observational studies with point or longitudinal treatments by easing and extending the functionality of the R packages 'twang' for generalized boosted modeling (McCaffrey, Ridgeway & Morral, 2004) <doi:10.1037/1082-989X.9.4.403>, 'CBPS' for covariate balancing propensity score weighting (Imai & Ratkovic, 2014) <doi:10.1111/rssb.12027>, 'ebal' for entropy balancing (Hainmueller, 2012) <doi:10.1093/pan/mpr025>, 'optweight' for optimization-based weights (Zubizarreta, 2015) <doi:10.1080/01621459.2015.1023805>, 'ATE' for empirical balancing calibration weighting (Chan, Yam, & Zhang, 2016) <doi:10.1111/rssb.12129>, and 'SuperLearner' for stacked machine learning-based propensity scores (Pirracchio, Petersen, & van der Laan, 2015) <doi:10.1093/aje/kwu253>. Also allows for assessment of weights and checking of covariate balance by interfacing directly with 'cobalt'.
Author: Noah Greifer [aut, cre] (<https://orcid.org/0000-0003-3067-7154>)
Maintainer: Noah Greifer <noah.greifer@gmail.com>
Diff between WeightIt versions 0.8.0 dated 2020-01-12 and 0.9.0 dated 2020-02-11
DESCRIPTION | 8 MD5 | 38 +- NAMESPACE | 1 NEWS.md | 10 R/functions_for_processing.R | 284 +++++++++++++++++---- R/weightit.R | 61 ++-- R/weightit.fit.R | 16 - R/weightit2method.R | 473 +++++++++++++++++++++--------------- R/weightitMSM.R | 83 +++--- README.md | 1 build/partial.rdb |binary build/vignette.rds |binary inst/doc/WeightIt_A0_basic_use.html | 78 +++-- man/get_w_from_ps.Rd | 6 man/method-cbps.Rd | 9 man/method-ebal.Rd | 30 +- man/method-gbm.Rd | 2 man/method-super.Rd | 41 ++- man/summary.weightit.Rd | 5 man/weightit.Rd | 1 20 files changed, 775 insertions(+), 372 deletions(-)
Title: Base Package for Phylogenetic Structures and Comparative Data
Description: Provides a base S4 class for comparative methods, incorporating
one or more trees and trait data.
Author: R Hackathon et al. (alphabetically: Ben Bolker, Marguerite Butler,
Peter Cowan, Damien de Vienne, Dirk Eddelbuettel, Mark Holder, Thibaut
Jombart, Steve Kembel, Francois Michonneau, David Orme, Brian O'Meara,
Emmanuel Paradis, Jim Regetz, Derrick Zwickl)
Maintainer: Francois Michonneau <francois.michonneau@gmail.com>
Diff between phylobase versions 0.8.6 dated 2019-02-02 and 0.8.8 dated 2020-02-11
phylobase-0.8.6/phylobase/vignettes/auto |only phylobase-0.8.8/phylobase/DESCRIPTION | 8 +- phylobase-0.8.8/phylobase/MD5 | 48 ++++++-------- phylobase-0.8.8/phylobase/NEWS.md | 5 + phylobase-0.8.8/phylobase/R/ancestors.R | 2 phylobase-0.8.8/phylobase/build/vignette.rds |binary phylobase-0.8.8/phylobase/inst/doc/phylobase.pdf |binary phylobase-0.8.8/phylobase/man/MRCA.Rd | 1 phylobase-0.8.8/phylobase/man/addData-methods.Rd | 25 +++++-- phylobase-0.8.8/phylobase/man/ancestors.Rd | 3 phylobase-0.8.8/phylobase/man/edgeLength-methods.Rd | 3 phylobase-0.8.8/phylobase/man/formatData.Rd | 17 +++- phylobase-0.8.8/phylobase/man/getNode-methods.Rd | 33 +++++++-- phylobase-0.8.8/phylobase/man/labels-methods.Rd | 6 - phylobase-0.8.8/phylobase/man/phylo4-methods.Rd | 15 ++-- phylobase-0.8.8/phylobase/man/phylo4d-methods.Rd | 43 +++++++++--- phylobase-0.8.8/phylobase/man/phylobubbles.Rd | 20 ++++- phylobase-0.8.8/phylobase/man/plotOneTree.Rd | 13 +++ phylobase-0.8.8/phylobase/man/print-methods.Rd | 4 - phylobase-0.8.8/phylobase/man/readNexus.Rd | 58 ++++++++++++----- phylobase-0.8.8/phylobase/man/subset-methods.Rd | 12 ++- phylobase-0.8.8/phylobase/man/tdata-methods.Rd | 18 +++-- phylobase-0.8.8/phylobase/man/tip.data.plot.Rd | 17 +++- phylobase-0.8.8/phylobase/man/treePlot-methods.Rd | 24 +++++-- phylobase-0.8.8/phylobase/man/treeStructure-methods.Rd | 1 25 files changed, 254 insertions(+), 122 deletions(-)
Title: Multivariate Meshes and Histograms in Arbitrary Dimensions
Description: Define, manipulate and plot meshes on simplices, spheres, balls, rectangles and tubes.
Directional and other multivariate histograms are provided.
Author: John P. Nolan
Maintainer: John P. Nolan <jpnolan@american.edu>
Diff between mvmesh versions 1.5 dated 2017-09-16 and 1.6 dated 2020-02-11
DESCRIPTION | 8 ++++---- MD5 | 10 +++++----- R/mvhist.R | 3 ++- R/mvmesh.R | 45 +++++++++++++++++++++++++++------------------ man/mvmesh-geom.Rd | 8 ++++---- man/mvmesh-package.Rd | 1 + 6 files changed, 43 insertions(+), 32 deletions(-)
Title: Multi-Parent Population QTL Analysis
Description: Analysis of experimental multi-parent populations to detect
regions of the genome (called quantitative trait loci, QTLs)
influencing phenotypic traits. The population must be composed of crosses
between a set of at least three parents (e.g. factorial design,
'diallel', or nested association mapping). The functions cover data
processing, QTL detection, and results visualization. The implemented
methodology is described by Garin, Wimmer, Mezmouk, Malosetti and
van Eeuwijk (2017) <doi:10.1007/s00122-017-2923-3>.
Author: Vincent Garin [aut, cre],
Valentin Wimmer [aut],
Dietrich Borchardt [ctb, dtc],
Fred van Eeuwijk [ctb, ths],
Marcos Malosetti [ctb, ths]
Maintainer: Vincent Garin <vincent.garin6@gmail.com>
Diff between mppR versions 1.2.0 dated 2019-05-31 and 1.2.1 dated 2020-02-11
mppR-1.2.0/mppR/vignettes/figures/gen_eff.pdf |only mppR-1.2.1/mppR/DESCRIPTION | 10 mppR-1.2.1/mppR/MD5 | 36 +-- mppR-1.2.1/mppR/NEWS.md | 6 mppR-1.2.1/mppR/R/IBS.mppData.R | 281 ++++++++++++------------- mppR-1.2.1/mppR/R/IncMat_QTL_MAF.R | 8 mppR-1.2.1/mppR/R/QC.mppData.R | 4 mppR-1.2.1/mppR/R/check_IBS.R | 142 ++++++------ mppR-1.2.1/mppR/R/color.code.R | 142 +++++++----- mppR-1.2.1/mppR/R/create.mppData.R | 2 mppR-1.2.1/mppR/R/plot.QTLprof.R | 26 +- mppR-1.2.1/mppR/build/vignette.rds |binary mppR-1.2.1/mppR/inst/CITATION | 2 mppR-1.2.1/mppR/inst/doc/mppR_vignette.R | 5 mppR-1.2.1/mppR/inst/doc/mppR_vignette.pdf |binary mppR-1.2.1/mppR/inst/doc/mppR_vignette.rnw | 21 - mppR-1.2.1/mppR/man/IBS.mppData.Rd | 50 ---- mppR-1.2.1/mppR/man/plot.QTLprof.Rd | 18 - mppR-1.2.1/mppR/vignettes/figures/gen_eff2.pdf |only mppR-1.2.1/mppR/vignettes/mppR_vignette.rnw | 21 - 20 files changed, 390 insertions(+), 384 deletions(-)
Title: Nonparametric Item Response Theory
Description: Fits nonparametric item and option characteristic curves using kernel smoothing. It allows for optimal selection of the smoothing bandwidth using cross-validation and a variety of exploratory plotting tools. The kernel smoothing is based on methods described in Silverman, B.W. (1986). Density Estimation for Statistics and Data Analysis. Chapman & Hall, London.
Author: Angelo Mazza, Antonio Punzo, Brian McGuire
Maintainer: Brian McGuire <mcguirebc@gmail.com>
Diff between KernSmoothIRT versions 6.2 dated 2019-08-21 and 6.3 dated 2020-02-11
DESCRIPTION | 10 MD5 | 8 NAMESPACE | 1 R/Inputcheck.R | 2 R/ksIRT.R | 576 ++++++++++++++++++++++++++++----------------------------- 5 files changed, 299 insertions(+), 298 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-09-19 2.1.2
2017-10-18 2.1.1
2017-10-10 2.1.0
2013-09-09 2.0-4
2012-12-07 2.0-3
Title: Multivariate Meta-Analysis
Description: Functions to run fixed effects or random effects multivariate meta-analysis.
Author: Han Chen
Maintainer: Han Chen <Han.Chen.2@uth.tmc.edu>
Diff between mvtmeta versions 1.0 dated 2012-07-10 and 1.1 dated 2020-02-11
DESCRIPTION | 21 ++++++++++----------- MD5 | 12 ++++++------ NAMESPACE | 1 + R/mvtmeta_fe.R | 4 ++-- man/mvtmeta-package.Rd | 10 ++++------ man/mvtmeta_fe.Rd | 3 +-- man/mvtmeta_re.Rd | 3 +-- 7 files changed, 25 insertions(+), 29 deletions(-)
Title: Geostatistical Analysis in R
Description: Implements common geostatistical methods in a clean, straightforward, efficient manner. The methods are discussed in Schabenberger and Gotway (2004, <ISBN:9781584883227>) and Waller and Gotway (2004, <ISBN:9780471387718>). This package is a quasi-reboot of the 'SpatialTools' package.
Author: Joshua French
Maintainer: Joshua French <joshua.french@ucdenver.edu>
Diff between gear versions 0.1.4 dated 2019-06-14 and 0.1.5 dated 2020-02-11
DESCRIPTION | 12 MD5 | 35 +- NEWS |only R/cmod.std.R | 164 +++++----- man/geolm.Rd | 12 man/mle.Rd | 14 man/plot.vgram.Rd | 2 man/predict.geolmMan.Rd | 3 man/predict.geolmStd.Rd | 3 man/vgram.Rd | 15 man/vgram_check_args.Rd | 3 tests/test-all.R | 15 tests/testthat/test-eval-cmod-cmodStd.R | 204 ++++++------ tests/testthat/test-mle-geolmStd.R | 125 +++---- tests/testthat/test-predict-geolmMan-sim.R | 164 +++++----- tests/testthat/test-predict-geolmMan.R | 152 ++++----- tests/testthat/test-predict-geolmStd-sim.R | 464 ++++++++++++++--------------- tests/testthat/test-predict-geolmStd.R | 369 +++++++++++------------ tests/testthat/test-vgram.R | 200 ++++++------ 19 files changed, 981 insertions(+), 975 deletions(-)
Title: Dynamic Modeling in R
Description: Intensive longitudinal data have become increasingly prevalent in
various scientific disciplines. Many such data sets are noisy, multivariate,
and multi-subject in nature. The change functions may also be continuous, or
continuous but interspersed with periods of discontinuities (i.e., showing
regime switches). The package 'dynr' (Dynamic Modeling in R) is an R package
that implements a set of computationally efficient algorithms for handling a
broad class of linear and nonlinear discrete- and continuous-time models with
regime-switching properties under the constraint of linear Gaussian measurement
functions. The discrete-time models can generally take on the form of a state-
space or difference equation model. The continuous-time models are generally
expressed as a set of ordinary or stochastic differential equations. All
estimation and computations are performed in C, but users are provided with the
option to specify the model of interest via a set of simple and easy-to-learn
model specification functions in R. Model fitting can be performed using single-
subject time series data or multiple-subject longitudinal data.
Author: Lu Ou [aut],
Michael D. Hunter [aut, cre] (<https://orcid.org/0000-0002-3651-6709>),
Sy-Miin Chow [aut] (<https://orcid.org/0000-0003-1938-027X>),
Linying Ji [aut],
Meng Chen [aut],
Hui-Ju Hung [aut],
Jungmin Lee [aut],
Yanling Li [aut],
Jonathan Park [aut]
Maintainer: Michael D. Hunter <mhunter.ou@gmail.com>
Diff between dynr versions 0.1.15-1 dated 2019-10-05 and 0.1.15-25 dated 2020-02-11
DESCRIPTION | 26 - MD5 | 42 - R/dynrCook.R | 6 R/dynrMi.R | 2 R/dynrModel.R | 12 R/dynrRecipe.R | 14 R/dynrVersion.R | 2 README.md | 2 build/partial.rdb |binary data/vdpData.rda |binary demo/VDPwithRand.R | 6 inst/doc/InstallationForDevelopers.pdf |binary inst/doc/InstallationForUsers.pdf |binary inst/doc/LinearDiscreteTimeModels.pdf |binary inst/doc/NonlinearContinuousTimeModels.pdf |binary inst/models/passing/LinearSDEWithChecks.R | 7 inst/models/passing/errorCheckDyn.R | 17 src/adaodesolver.c | 686 ++++++++++++++--------------- src/model.c | 123 ++--- src/model.h | 19 src/numeric_derivatives.c | 135 ++--- src/print_function.c | 56 +- 22 files changed, 614 insertions(+), 541 deletions(-)
Title: An R Plug-in for the Distributed Hydrological Model GEOtop
Description: It analyzes raster maps and other information as input/output
files from the Hydrological Distributed Model GEOtop. It contains functions
and methods to import maps and other keywords from geotop.inpts file. Some
examples with simulation cases of GEOtop 2.x/3.x are presented in the package.
Any information about the GEOtop Distributed Hydrological Model source code
is available on www.geotop.org. Technical details about the model are
available in Endrizzi et al, 2014
(<http://www.geosci-model-dev.net/7/2831/2014/gmd-7-2831-2014.html>).
Author: Emanuele Cordano, Daniele Andreis, Fabio Zottele
Maintainer: Emanuele Cordano <emanuele.cordano@gmail.com>
Diff between geotopbricks versions 1.5.3 dated 2019-03-21 and 1.5.4 dated 2020-02-11
DESCRIPTION | 10 +++++----- MD5 | 18 +++++++++--------- R/max_value.R | 8 ++++---- R/min_value.R | 8 ++++---- R/writeRasterxgeotop.R | 4 ++-- data/bondone.rda |binary man/bondone.Rd | 4 ++-- man/max_value.Rd | 6 +++--- man/min_value.Rd | 6 +++--- man/writeRasterxGEOtop.Rd | 4 ++-- 10 files changed, 34 insertions(+), 34 deletions(-)
Title: Activity Fragmentation Metrics Extracted from Minute Level
Activity Data
Description: Recent studies haven shown that, on top of total daily active/sedentary volumes, the time
accumulation strategies provide more sensitive information. This package provides functions to extract
commonly used fragmentation metrics to quantify such time accumulation strategies based on minute level
actigraphy-measured activity counts data.
Author: Junrui Di [aut, cre],
John Muschelli [aut],
Vadim zipunnikov [aut]
Maintainer: Junrui Di <dijunrui@gmail.com>
Diff between ActFrag versions 0.1.0 dated 2019-06-28 and 0.1.1 dated 2020-02-11
DESCRIPTION | 8 MD5 | 19 + NEWS.md |only R/fragmentation.R | 2 R/fragmentation_long.R | 450 +++++++++++++++++++++++----------------------- README.md | 1 build/vignette.rds |binary inst/doc/ActFrag.R | 12 - inst/doc/ActFrag.html | 9 man/fragmentation.Rd | 11 - man/fragmentation_long.Rd | 17 + 11 files changed, 272 insertions(+), 257 deletions(-)
Title: Compositional Data Analysis
Description: Methods for analysis of compositional data including robust
methods (<doi:10.1007/978-3-319-96422-5>), imputation of missing values (<doi:10.1016/j.csda.2009.11.023>), methods to replace
rounded zeros (<doi:10.1080/02664763.2017.1410524>, <doi:10.1016/j.chemolab.2016.04.011>, <doi:10.1016/j.csda.2012.02.012>),
count zeros (<doi:10.1177/1471082X14535524>),
methods to deal with essential zeros (<doi:10.1080/02664763.2016.1182135>), (robust) outlier
detection for compositional data, (robust) principal component analysis for
compositional data, (robust) factor analysis for compositional data, (robust)
discriminant analysis for compositional data (Fisher rule), robust regression
with compositional predictors, functional data analysis and p-splines (<doi:10.1016/j.csda.2015.07.007>),
contingency (<doi:10.1080/03610926.2013.824980>)
and compositional tables (<doi:10.1111/sjos.12326>, <doi:10.1111/sjos.12223>, <doi:10.1080/02664763.2013.856871>)
and (robust) Anderson-Darling normality tests for
compositional data as well as popular log-ratio transformations (addLR, cenLR,
isomLR, and their inverse transformations). In addition, visualisation and
diagnostic tools are implemented as well as high and low-level plot functions
for the ternary diagram.
Author: Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>),
Karel Hron [aut] (<https://orcid.org/0000-0002-1847-6598>),
Peter Filzmoser [aut] (<https://orcid.org/0000-0002-8014-4682>),
Kamila Facevicova [ctb],
Petra Kynclova [ctb],
Jan Walach [ctb],
Veronika Pintar [ctb],
Jiajia Chen [ctb],
Dominika Miksova [ctb],
Bernhard Meindl [ctb],
Alessandra Menafoglio [ctb] (<https://orcid.org/0000-0003-0682-6412>),
Alessia Di Blasi [ctb],
Federico Pavone [ctb],
Gianluca Zeni [ctb]
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between robCompositions versions 2.2.0 dated 2020-01-14 and 2.2.1 dated 2020-02-11
DESCRIPTION | 20 +++++++++++--------- MD5 | 26 +++++++++++++------------- NEWS | 3 +++ R/compareMahal.R | 4 ++-- R/splineDensity.R | 2 ++ R/splineDensity.smoothingSplinesValidation.R | 2 ++ data/nutrients.rda |binary data/nutrients_branded.rda |binary inst/doc/imputation.pdf |binary inst/doc/robCompositions-overview.pdf |binary man/plot.smoothSpl.Rd | 3 +++ man/smoothSplines.Rd | 5 +++++ man/smoothSplinesVal.Rd | 5 +++++ tests/testthat/test_iris.r | 22 +++++++++++----------- 14 files changed, 57 insertions(+), 35 deletions(-)
More information about robCompositions at CRAN
Permanent link
Title: R Individual Specialization (RInSp)
Description: Functions to calculate several ecological indices of individual
and population niche width (Araujo's E, clustering and pairwise similarity
among individuals, IS, Petraitis' W, and Roughgarden's WIC/TNW) to assess
individual specialization based on data of resource use. Resource use can
be quantified by counts of categories, measures of mass or length, or
proportions. Monte Carlo resampling procedures are available for hypothesis
testing against multinomial null models.
Author: Dr. Nicola Zaccarelli [aut, cre],
Giorgio Mancinelli [aut],
Dan Bolnick [ctb]
Maintainer: Dr. Nicola Zaccarelli <nicola.zaccarelli@gmail.com>
Diff between RInSp versions 1.2.3 dated 2018-01-24 and 1.2.4 dated 2020-02-11
DESCRIPTION | 31 ++-- MD5 | 66 ++++----- R/Eindex.R | 359 +++++++++++++++++++++++++-------------------------- R/Emc.R | 170 ++++++++++++------------ R/Hier2L.R | 37 ++--- R/MCp.RInSp.r | 13 - R/Null.Hp.RInSp.R | 20 +- R/PSicalc.R | 96 +++++++------ R/RInSp2vegan.r | 53 +++---- R/WTcMC.R | 23 +-- R/WTdMC.R | 28 +-- R/import.RInSp.R | 176 +++++++++++++------------ R/like.Wi.R | 27 +-- R/nodf.r | 31 ++-- R/overlap.r | 25 +-- R/pop.diet.R | 16 +- R/sumMC.RInSp.R | 95 ++++++------- man/Emc.Rd | 184 +++++++++++++------------- man/Hier2L.Rd | 4 man/MCp.RInSp.Rd | 130 +++++++++--------- man/NODF.Rd | 124 ++++++++--------- man/Null.Hp.RInSp.Rd | 16 +- man/PSicalc.Rd | 144 ++++++++++---------- man/RInSp-package.Rd | 167 ++++++++++++----------- man/RinSp2vegan.Rd | 72 +++++----- man/Trout.Rd | 78 +++++------ man/WTcMC.Rd | 164 +++++++++++------------ man/WTdMC.Rd | 8 - man/import.RInSp.Rd | 155 +++++++++++----------- man/like.Wi.Rd | 112 +++++++-------- man/overlap.Rd | 15 +- man/pop.diet.Rd | 4 man/sumMC.RInSp.Rd | 68 ++++----- src/CPSicalc.c | 17 +- 34 files changed, 1394 insertions(+), 1334 deletions(-)
Title: Calculate Pairwise Distances
Description: A common framework for calculating distance matrices.
Author: Nello Blaser [aut, cre]
Maintainer: Nello Blaser <nello.blaser@uib.no>
Diff between rdist versions 0.0.3 dated 2018-05-18 and 0.0.4 dated 2020-02-11
DESCRIPTION | 8 - MD5 | 60 +++++------ NAMESPACE | 28 ++--- NEWS.md | 73 +++++++------ R/FUN_distances.R | 52 ++++----- R/correlation_distances.R | 74 +++++++------- R/distance_functions.r | 194 ++++++++++++++++++------------------- R/farthest_point_sampling.R | 100 +++++++++---------- R/is_metric.R | 116 +++++++++++----------- R/product_metric.R | 76 +++++++------- R/rdist-package.r | 70 ++++++------- README.md | 54 +++++----- man/farthest_point_sampling.Rd | 81 ++++++++------- man/is_metric.Rd | 58 +++++------ man/product_metric.Rd | 58 +++++------ man/rdist.Rd | 98 +++++++++--------- src/Makevars | 2 src/Makevars.win | 2 src/RcppExports.cpp | 12 +- src/dist.cpp | 6 - src/dist.h | 6 - tests/testthat.R | 8 - tests/testthat/test-canberra.R | 34 +++--- tests/testthat/test-correlation.R | 98 +++++++++--------- tests/testthat/test-euclidean.R | 82 +++++++-------- tests/testthat/test-hamming.R | 48 ++++----- tests/testthat/test-jaccard.R | 60 +++++------ tests/testthat/test-manhattan.R | 34 +++--- tests/testthat/test-maximum.R | 34 +++--- tests/testthat/test-minkowski.R | 94 ++++++++--------- tests/testthat/test-user-defined.R | 106 ++++++++++---------- 31 files changed, 917 insertions(+), 909 deletions(-)
Title: Decision Tree Analysis for Probabilistic Subgroup Identification
with Multiple Treatments
Description: In the situation when multiple alternative treatments or
interventions available, different population groups may respond differently
to different treatments. This package implements a method that discovers
the population subgroups in which a certain treatment has a better effect
than the other alternative treatments. This is done by first estimating the
treatment effect for a given treatment and its uncertainty by computing random
forests, and the resulting model is summarized by a decision tree in which the
probabilities that the given treatment is best for a given subgroup is shown in
the corresponding terminal node of the tree.
Author: Oleg Sysoev, Krzysztof Bartoszek, Katarina Ekholm Selling and Lotta
Ekstrom
Maintainer: Oleg Sysoev <Oleg.Sysoev@liu.se>
Diff between psica versions 1.0.1 dated 2018-11-29 and 1.0.2 dated 2020-02-11
DESCRIPTION | 8 ++++---- MD5 | 12 ++++++------ R/psica.R | 1 - build/partial.rdb |binary inst/CITATION | 10 ++++++---- inst/REFERENCES.bib | 26 +++++++++++--------------- man/snip.psicaTree.Rd | 2 -- 7 files changed, 27 insertions(+), 32 deletions(-)
Title: Tools for Eurostat Open Data
Description: Tools to download data from the Eurostat database
<http://ec.europa.eu/eurostat> together with search and
manipulation utilities.
Author: Leo Lahti [aut, cre] (<https://orcid.org/0000-0001-5537-637X>),
Janne Huovari [aut],
Markus Kainu [aut],
Przemyslaw Biecek [aut],
Joona Lehtomaki [ctb],
Francois Briatte [ctb],
Oliver Reiter [ctb]
Maintainer: Leo Lahti <leo.lahti@iki.fi>
Diff between eurostat versions 3.5.2 dated 2020-01-25 and 3.6.1 dated 2020-02-11
eurostat-3.5.2/eurostat/tests/testthat/test-all.R |only eurostat-3.6.1/eurostat/DESCRIPTION | 10 eurostat-3.6.1/eurostat/MD5 | 49 ++- eurostat-3.6.1/eurostat/NAMESPACE | 14 + eurostat-3.6.1/eurostat/NEWS | 6 eurostat-3.6.1/eurostat/R/add_nuts_level.R |only eurostat-3.6.1/eurostat/R/data_nuts_correspondence.R |only eurostat-3.6.1/eurostat/R/data_regional_changes_2016.R |only eurostat-3.6.1/eurostat/R/get_eurostat.R | 132 ++++------ eurostat-3.6.1/eurostat/R/get_eurostat_geospatial.R | 73 +++-- eurostat-3.6.1/eurostat/R/get_eurostat_json.R | 111 ++++---- eurostat-3.6.1/eurostat/R/get_eurostat_raw.R | 2 eurostat-3.6.1/eurostat/R/harmonize_geo_code.R |only eurostat-3.6.1/eurostat/R/recode_to_nuts_2013.R |only eurostat-3.6.1/eurostat/R/recode_to_nuts_2016.R |only eurostat-3.6.1/eurostat/R/utils.R | 16 + eurostat-3.6.1/eurostat/README.md | 91 ++---- eurostat-3.6.1/eurostat/data/datalist | 2 eurostat-3.6.1/eurostat/data/nuts_correspondence.rda |only eurostat-3.6.1/eurostat/data/regional_changes_2016.rda |only eurostat-3.6.1/eurostat/inst/doc/vignette.html | 4 eurostat-3.6.1/eurostat/man/add_nuts_level.Rd |only eurostat-3.6.1/eurostat/man/harmonize_geo_code.Rd |only eurostat-3.6.1/eurostat/man/nuts_correspondence.Rd |only eurostat-3.6.1/eurostat/man/recode_to_nuts_2013.Rd |only eurostat-3.6.1/eurostat/man/recode_to_nuts_2016.Rd |only eurostat-3.6.1/eurostat/man/regional_changes_2016.Rd |only eurostat-3.6.1/eurostat/tests/testthat/test_bibliography.R |only eurostat-3.6.1/eurostat/tests/testthat/test_cache.R |only eurostat-3.6.1/eurostat/tests/testthat/test_flags.R |only eurostat-3.6.1/eurostat/tests/testthat/test_get.R |only eurostat-3.6.1/eurostat/tests/testthat/test_json.R |only eurostat-3.6.1/eurostat/tests/testthat/test_label.R |only eurostat-3.6.1/eurostat/tests/testthat/test_misc.R |only eurostat-3.6.1/eurostat/tests/testthat/test_regional.R |only eurostat-3.6.1/eurostat/tests/testthat/test_search.R |only eurostat-3.6.1/eurostat/vignettes/website/eurostat_tutorial.Rmd | 12 eurostat-3.6.1/eurostat/vignettes/website/regional_data.Rmd |only 38 files changed, 301 insertions(+), 221 deletions(-)
Title: Data Analysis using Bootstrap-Coupled Estimation
Description: Data Analysis using Bootstrap-Coupled ESTimation.
Estimation statistics is a simple framework that avoids the pitfalls of
significance testing. It uses familiar statistical concepts: means,
mean differences, and error bars. More importantly, it focuses on the
effect size of one's experiment/intervention, as opposed to a false
dichotomy engendered by P values.
An estimation plot has two key features:
1. It presents all datapoints as a swarmplot, which orders each point to
display the underlying distribution.
2. It presents the effect size as a bootstrap 95% confidence interval on a
separate but aligned axes.
Estimation plots are introduced in Ho et al., Nature Methods 2019, 1548-7105.
<doi:10.1038/s41592-019-0470-3>.
The free-to-view PDF is located at <https://rdcu.be/bHhJ4>.
Author: Joses W. Ho [cre, aut],
Tayfun Tumkaya [aut]
Maintainer: Joses W. Ho <joseshowh@gmail.com>
Diff between dabestr versions 0.2.2 dated 2019-07-04 and 0.2.3 dated 2020-02-11
dabestr-0.2.2/dabestr/inst/doc/bootstrap-confidence-intervals.R |only dabestr-0.2.2/dabestr/inst/doc/bootstrap-confidence-intervals.Rmd |only dabestr-0.2.2/dabestr/inst/doc/bootstrap-confidence-intervals.html |only dabestr-0.2.2/dabestr/inst/doc/robust-statistical-visualization.R |only dabestr-0.2.2/dabestr/inst/doc/robust-statistical-visualization.Rmd |only dabestr-0.2.2/dabestr/inst/doc/robust-statistical-visualization.html |only dabestr-0.2.2/dabestr/tests/testthat/Rplots.pdf |only dabestr-0.2.2/dabestr/vignettes/bootstrap-confidence-intervals.Rmd |only dabestr-0.2.2/dabestr/vignettes/robust-statistical-visualization.Rmd |only dabestr-0.2.3/dabestr/DESCRIPTION | 10 - dabestr-0.2.3/dabestr/LICENSE | 2 dabestr-0.2.3/dabestr/MD5 | 39 ++---- dabestr-0.2.3/dabestr/NEWS.md | 3 dabestr-0.2.3/dabestr/R/main.R | 11 - dabestr-0.2.3/dabestr/R/plot_helpers.R | 45 ++++--- dabestr-0.2.3/dabestr/README.md | 46 +++---- dabestr-0.2.3/dabestr/build/vignette.rds |binary dabestr-0.2.3/dabestr/inst/CITATION | 8 - dabestr-0.2.3/dabestr/inst/doc/using-dabestr.R | 35 +++-- dabestr-0.2.3/dabestr/inst/doc/using-dabestr.Rmd | 32 +++-- dabestr-0.2.3/dabestr/inst/doc/using-dabestr.html | 60 +++++----- dabestr-0.2.3/dabestr/man/dabest.Rd | 25 ++-- dabestr-0.2.3/dabestr/man/dabestr.Rd | 1 dabestr-0.2.3/dabestr/man/plot.dabest.Rd | 32 +++-- dabestr-0.2.3/dabestr/vignettes/using-dabestr.Rmd | 32 +++-- 25 files changed, 210 insertions(+), 171 deletions(-)
Title: Interface to Species Occurrence Data Sources
Description: A programmatic interface to many species occurrence data sources,
including Global Biodiversity Information Facility ('GBIF'), 'USGSs'
Biodiversity Information Serving Our Nation ('BISON'), 'iNaturalist',
Berkeley 'Ecoinformatics' Engine, 'eBird', Integrated Digitized
'Biocollections' ('iDigBio'), 'VertNet', Ocean 'Biogeographic' Information
System ('OBIS'), and Atlas of Living Australia ('ALA'). Includes
functionality for retrieving species occurrence data, and combining
those data.
Author: Scott Chamberlain [aut, cre] (<https://orcid.org/0000-0003-1444-9135>),
Karthik Ram [ctb],
Ted Hart [ctb],
rOpenSci [fnd] (https://ropensci.org/)
Maintainer: Scott Chamberlain <myrmecocystus@gmail.com>
Diff between spocc versions 1.0.2 dated 2019-11-02 and 1.0.8 dated 2020-02-11
spocc-1.0.2/spocc/vignettes/img |only spocc-1.0.8/spocc/DESCRIPTION | 12 spocc-1.0.8/spocc/LICENSE | 2 spocc-1.0.8/spocc/MD5 | 78 spocc-1.0.8/spocc/NEWS.md | 9 spocc-1.0.8/spocc/R/as.vertnet.R | 24 spocc-1.0.8/spocc/R/occ_names.R | 6 spocc-1.0.8/spocc/R/plugins.r | 7 spocc-1.0.8/spocc/README.md | 124 spocc-1.0.8/spocc/build/vignette.rds |binary spocc-1.0.8/spocc/inst/doc/spocc.Rmd | 330 -- spocc-1.0.8/spocc/inst/doc/spocc.html | 330 -- spocc-1.0.8/spocc/man/as.ala.Rd | 12 spocc-1.0.8/spocc/man/as.bison.Rd | 12 spocc-1.0.8/spocc/man/as.ecoengine.Rd | 12 spocc-1.0.8/spocc/man/as.gbif.Rd | 12 spocc-1.0.8/spocc/man/as.idigbio.Rd | 12 spocc-1.0.8/spocc/man/as.inat.Rd | 12 spocc-1.0.8/spocc/man/as.obis.Rd | 12 spocc-1.0.8/spocc/man/as.vertnet.Rd | 36 spocc-1.0.8/spocc/man/bbox2wkt.Rd | 6 spocc-1.0.8/spocc/man/obis_search.Rd | 24 spocc-1.0.8/spocc/man/occ.Rd | 44 spocc-1.0.8/spocc/man/occ_names.Rd | 21 spocc-1.0.8/spocc/man/occ_names_options.Rd | 8 spocc-1.0.8/spocc/man/occ_options.Rd | 8 spocc-1.0.8/spocc/man/spocc-package.Rd | 2 spocc-1.0.8/spocc/man/spocc_objects.Rd | 8 spocc-1.0.8/spocc/man/wkt_vis.Rd | 3 spocc-1.0.8/spocc/tests/fixtures/occ2df.yml | 285 +- spocc-1.0.8/spocc/tests/fixtures/occ2df_with_eventdate_gone.yml | 1241 ++++------ spocc-1.0.8/spocc/tests/fixtures/occ_options_bison.yml | 11 spocc-1.0.8/spocc/tests/fixtures/occ_options_ebird.yml |only spocc-1.0.8/spocc/tests/fixtures/occ_options_ecoengine.yml |only spocc-1.0.8/spocc/tests/fixtures/occ_options_gbif.yml |only spocc-1.0.8/spocc/tests/fixtures/occ_vertnet.yml | 251 +- spocc-1.0.8/spocc/tests/testthat/test-has_coords.R | 4 spocc-1.0.8/spocc/tests/testthat/test-occ2df.R | 7 spocc-1.0.8/spocc/tests/testthat/test-options.R | 34 spocc-1.0.8/spocc/vignettes/spocc.Rmd | 330 -- 40 files changed, 1442 insertions(+), 1887 deletions(-)
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>
Diff between rqdatatable versions 1.2.6 dated 2020-01-29 and 1.2.7 dated 2020-02-11
rqdatatable-1.2.6/rqdatatable/R/rexp_rquery.R |only rqdatatable-1.2.7/rqdatatable/DESCRIPTION | 12 - rqdatatable-1.2.7/rqdatatable/MD5 | 97 ++++---- rqdatatable-1.2.7/rqdatatable/NAMESPACE | 96 -------- rqdatatable-1.2.7/rqdatatable/NEWS.md | 6 rqdatatable-1.2.7/rqdatatable/R/data_table_exports.R | 4 rqdatatable-1.2.7/rqdatatable/R/relop_drop_columns.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_extend.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_natural_join.R | 4 rqdatatable-1.2.7/rqdatatable/R/relop_non_sql.R | 20 - rqdatatable-1.2.7/rqdatatable/R/relop_null_replace.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_order_expr.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_orderby.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_project.R | 10 rqdatatable-1.2.7/rqdatatable/R/relop_rename_columns.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_select_columns.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_select_rows.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_set_indicator.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_sql.R | 4 rqdatatable-1.2.7/rqdatatable/R/relop_table_source.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_theta_join.R | 2 rqdatatable-1.2.7/rqdatatable/R/relop_unionall.R | 2 rqdatatable-1.2.7/rqdatatable/R/rquery_fns.R | 114 ---------- rqdatatable-1.2.7/rqdatatable/R/zzz.R | 4 rqdatatable-1.2.7/rqdatatable/README.md | 12 - rqdatatable-1.2.7/rqdatatable/build/vignette.rds |binary rqdatatable-1.2.7/rqdatatable/inst/doc/GroupedSampling.html | 75 +++--- rqdatatable-1.2.7/rqdatatable/inst/doc/R_mapping.html | 12 - rqdatatable-1.2.7/rqdatatable/inst/doc/logisticexample.html | 12 - rqdatatable-1.2.7/rqdatatable/man/ex_data_table.Rd | 4 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.Rd | 4 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_drop_columns.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_extend.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_natural_join.Rd | 4 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_non_sql.Rd | 4 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_null_replace.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_order_expr.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_orderby.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_project.Rd | 10 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_rename_columns.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_select_columns.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_select_rows.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_set_indicator.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_sql.Rd | 4 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_table_source.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_theta_join.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/ex_data_table_step.relop_unionall.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/reexports.Rd | 56 ---- rqdatatable-1.2.7/rqdatatable/man/rq_df_funciton_node.Rd | 2 rqdatatable-1.2.7/rqdatatable/man/rq_df_grouped_funciton_node.Rd | 2 50 files changed, 181 insertions(+), 439 deletions(-)
Title: Quality Report Generation for MaxQuant and mzTab Results
Description: Generates Proteomics (PTX) quality control (QC) reports for shotgun LC-MS data analyzed with the
MaxQuant software suite (from .txt files) or mzTab files (ideally from OpenMS 'QualityControl' tool).
Reports are customizable (target thresholds, subsetting) and available in HTML or PDF format.
Published in J. Proteome Res., Proteomics Quality Control: Quality Control Software for MaxQuant Results (2015)
<doi:10.1021/acs.jproteome.5b00780>.
Author: Chris Bielow [aut, cre],
Juliane Schmachtenberg [ctb],
Swenja Wagner [ctb],
Patricia Scheil [ctb],
Tom Waschischek [ctb],
Guido Mastrobuoni [dtc, rev]
Maintainer: Chris Bielow <chris.bielow@bsc.fu-berlin.de>
Diff between PTXQC versions 1.0.1 dated 2020-02-02 and 1.0.2 dated 2020-02-11
DESCRIPTION | 17 - LICENSE |only MD5 | 19 - NEWS | 3 inst/doc/PTXQC-Basic_Guide_for_R_users.html | 234 +++++++++++++++- inst/doc/PTXQC-CustomizeReport.html | 234 +++++++++++++++- inst/doc/PTXQC-DragNDrop.html | 234 +++++++++++++++- inst/doc/PTXQC-FAQ.html | 240 +++++++++++++++-- inst/doc/PTXQC-Input_And_Output_Data.html | 224 +++++++++++++++- inst/doc/PTXQC-ListOfMetrics.html | 391 ++++++++++++++++++++-------- tests/testthat/test_computeQC.R | 4 11 files changed, 1399 insertions(+), 201 deletions(-)
Title: Analysis of Diversity
Description: Functions, data sets and examples for the calculation of various indices of biodiversity including species, functional and phylogenetic diversity. Part of the indices are expressed in terms of equivalent numbers of species. The package also provides ways to partition biodiversity across spatial or temporal scales (alpha, beta, gamma diversities). In addition to the quantification of biodiversity, ordination approaches are available which rely on diversity indices and allow the detailed identification of species, functional or phylogenetic differences between communities.
Author: Sandrine Pavoine
Maintainer: Sandrine Pavoine <sandrine.pavoine@mnhn.fr>
Diff between adiv versions 1.4 dated 2020-01-07 and 2.0 dated 2020-02-11
DESCRIPTION | 8 ++++---- MD5 | 19 ++++++++++++++----- R/DP.R |only R/betaTreeUniqueness.R |only build/partial.rdb |binary data/RutorGlacier.rda |only inst |only man/DP.Rd |only man/K.Rd | 6 +++--- man/RutorGlacier.Rd |only man/batcomm.Rd | 4 ++-- man/betaTreeUniqueness.Rd |only man/dsimcom.Rd | 7 ++----- vignettes |only 14 files changed, 25 insertions(+), 19 deletions(-)
Title: Data Exchange Between R and 'LabKey' Server
Description: The 'LabKey' client library for R makes it easy for R users to
load live data from a 'LabKey' Server, <http://www.labkey.com/>,
into the R environment for analysis, provided users have permissions
to read the data. It also enables R users to insert, update, and
delete records stored on a 'LabKey' Server, provided they have appropriate
permissions to do so.
Author: Peter Hussey
Maintainer: Cory Nathe <cnathe@labkey.com>
Diff between Rlabkey versions 2.3.3 dated 2019-11-04 and 2.3.4 dated 2020-02-11
Rlabkey-2.3.3/Rlabkey/build |only Rlabkey-2.3.3/Rlabkey/inst/doc/RlabkeyExample.Rnw |only Rlabkey-2.3.3/Rlabkey/inst/doc/RlabkeyExample.pdf |only Rlabkey-2.3.3/Rlabkey/vignettes |only Rlabkey-2.3.4/Rlabkey/DESCRIPTION | 8 - Rlabkey-2.3.4/Rlabkey/MD5 | 18 +--- Rlabkey-2.3.4/Rlabkey/NEWS | 7 + Rlabkey-2.3.4/Rlabkey/R/labkey.defaults.R | 88 ++++++++++++--------- Rlabkey-2.3.4/Rlabkey/R/labkey.transform.R | 91 +++++++++++++++++----- Rlabkey-2.3.4/Rlabkey/R/schemaObjects.R | 18 ---- Rlabkey-2.3.4/Rlabkey/man/Rlabkey-package.Rd | 4 Rlabkey-2.3.4/Rlabkey/man/labkey.setDefaults.Rd | 25 +++--- 12 files changed, 162 insertions(+), 97 deletions(-)
Title: Multi Environment Trials Analysis
Description: Performs stability analysis of multi-environment
trial data using parametric and non-parametric methods. Parametric
methods includes Additive Main Effects and Multiplicative Interaction
(AMMI) analysis by Gauch (2013) <doi:10.2135/cropsci2013.04.0241>,
Genotype plus Genotype-Environment (GGE) biplot analysis by Yan & Kang
(2003) <doi:10.1201/9781420040371>, joint Regression Analysis by
Eberhart & Russel (1966)
(<doi:10.2135/cropsci1966.0011183X000600010011x>), ecovalence by
Wricke (1965), genotypic confidence index by Annicchiarico (1992),
Murakami & Cruz's (2004) method <doi:10.12702/1984-7033.v04n01a02>,
stability variance by Shukla (1972) <doi:10.1038/hdy.1972.87>,
weighted average of absolute scores by Olivoto et al. (2019a)
<doi:10.2134/agronj2019.03.0220>, and multi-trait stability index by
Olivoto et al. (2019b) <doi:10.2134/agronj2019.03.0221>.
Non-parametric methods includes superiority index by Lin & Binns
(1988) <doi:10.4141/cjps88-018>, nonparametric measures of phenotypic
stability by Huehn (1990)
<https://link.springer.com/article/10.1007/BF00024241>, TOP third
statistic by Fox et al. (1990) <doi:10.1007/BF00040364>, geometric
adaptability index described by Shahbazi (2019)
<doi:10.1016/j.scienta.2019.04.047>. Functions for computing
biometrical analysis such as path analysis, canonical correlation,
partial correlation, clustering analysis, and tools for inspecting,
manipulating, summarizing and plotting typical multi-environment
trial data are also provided.
Author: Tiago Olivoto [aut, cre, cph] (<https://orcid.org/0000-0002-0241-9636>)
Maintainer: Tiago Olivoto <tiagoolivoto@gmail.com>
Diff between metan versions 1.2.1 dated 2020-01-14 and 1.3.0 dated 2020-02-11
metan-1.2.1/metan/R/as.split_factors.R |only metan-1.2.1/metan/R/gm_mean.R |only metan-1.2.1/metan/R/helper_mat.R |only metan-1.2.1/metan/R/hm_mean.R |only metan-1.2.1/metan/R/is.split_factors.R |only metan-1.2.1/metan/R/plot.FAI_BLUP.R |only metan-1.2.1/metan/R/plot.MTSI.R |only metan-1.2.1/metan/R/plot.can_cor.R |only metan-1.2.1/metan/R/plot.clustering.R |only metan-1.2.1/metan/R/plot.cvalidation.R |only metan-1.2.1/metan/R/plot.ge_cluster.R |only metan-1.2.1/metan/R/plot.ge_effects.R |only metan-1.2.1/metan/R/plot.ge_factanal.R |only metan-1.2.1/metan/R/plot.ge_reg.R |only metan-1.2.1/metan/R/plot.gge.R |only metan-1.2.1/metan/R/plot.performs_ammi.R |only metan-1.2.1/metan/R/plot.resp_surf.R |only metan-1.2.1/metan/R/plot.waas.R |only metan-1.2.1/metan/R/plot.waasb.R |only metan-1.2.1/metan/R/plot.wsmp.R |only metan-1.2.1/metan/R/predict.gge.R |only metan-1.2.1/metan/R/predict.performs_ammi.R |only metan-1.2.1/metan/R/predict.waas.R |only metan-1.2.1/metan/R/print.Ammi_indexes.R |only metan-1.2.1/metan/R/print.Annicchiarico.R |only metan-1.2.1/metan/R/print.Fox.R |only metan-1.2.1/metan/R/print.Shukla.R |only metan-1.2.1/metan/R/print.anova_ind.R |only metan-1.2.1/metan/R/print.anova_joint.R |only metan-1.2.1/metan/R/print.can_cor.R |only metan-1.2.1/metan/R/print.ecovalence.R |only metan-1.2.1/metan/R/print.gamem.R |only metan-1.2.1/metan/R/print.ge_factanal.R |only metan-1.2.1/metan/R/print.ge_reg.R |only metan-1.2.1/metan/R/print.ge_stats.R |only metan-1.2.1/metan/R/print.mtsi.R |only metan-1.2.1/metan/R/print.path_coeff.R |only metan-1.2.1/metan/R/print.performs_ammi.R |only metan-1.2.1/metan/R/print.superiority.R |only metan-1.2.1/metan/R/print.waas.R |only metan-1.2.1/metan/R/print.waasb.R |only metan-1.2.1/metan/R/sem.R |only metan-1.2.1/metan/inst/doc/vignettes_metan.R |only metan-1.2.1/metan/inst/doc/vignettes_metan.Rmd |only metan-1.2.1/metan/inst/doc/vignettes_metan.html |only metan-1.2.1/metan/man/as.split_factors.Rd |only metan-1.2.1/metan/man/desc_wider.Rd |only metan-1.2.1/metan/man/gm_mean.Rd |only metan-1.2.1/metan/man/hm_mean.Rd |only metan-1.2.1/metan/man/is.split_factors.Rd |only metan-1.2.1/metan/man/make_lower_tri.Rd |only metan-1.2.1/metan/man/make_sym.Rd |only metan-1.2.1/metan/man/make_upper_tri.Rd |only metan-1.2.1/metan/man/means_by.Rd |only metan-1.2.1/metan/man/sem.Rd |only metan-1.2.1/metan/vignettes/vignettes_metan.Rmd |only metan-1.3.0/metan/DESCRIPTION | 11 metan-1.3.0/metan/MD5 | 450 +-- metan-1.3.0/metan/NAMESPACE | 65 metan-1.3.0/metan/NEWS.md | 60 metan-1.3.0/metan/R/AMMI_indexes.R | 61 metan-1.3.0/metan/R/Annichiarico.R | 82 metan-1.3.0/metan/R/FAI_BLUP.R | 90 metan-1.3.0/metan/R/Fox.R | 67 metan-1.3.0/metan/R/Huehn.R | 9 metan-1.3.0/metan/R/MTSI.R | 154 + metan-1.3.0/metan/R/Schmildt.R | 13 metan-1.3.0/metan/R/Shukla.R | 67 metan-1.3.0/metan/R/Thennarasu.R | 9 metan-1.3.0/metan/R/WAASB.R | 1582 ++++++++----- metan-1.3.0/metan/R/anova_ind.R | 256 +- metan-1.3.0/metan/R/anova_joint.R | 262 +- metan-1.3.0/metan/R/arrange_ggplot.R | 2 metan-1.3.0/metan/R/as.lpcor.R | 4 metan-1.3.0/metan/R/can_cor.R | 645 ++--- metan-1.3.0/metan/R/clustering.R | 358 -- metan-1.3.0/metan/R/colindiag.R | 217 + metan-1.3.0/metan/R/comb_vars.R | 4 metan-1.3.0/metan/R/corr_ci.R | 94 metan-1.3.0/metan/R/corr_coef.R | 10 metan-1.3.0/metan/R/corr_ss.R | 3 metan-1.3.0/metan/R/covcor_design.R | 396 +-- metan-1.3.0/metan/R/cv_ammi.R | 199 + metan-1.3.0/metan/R/cv_ammif.R | 22 metan-1.3.0/metan/R/cv_blup.R | 99 metan-1.3.0/metan/R/desc_stat.R | 511 +--- metan-1.3.0/metan/R/desc_wider.R | 32 metan-1.3.0/metan/R/ecovalence.R | 66 metan-1.3.0/metan/R/env_dissimilarity.R | 10 metan-1.3.0/metan/R/find_outliers.R | 400 +-- metan-1.3.0/metan/R/gafem.R |only metan-1.3.0/metan/R/gai.R | 14 metan-1.3.0/metan/R/gamem.R | 571 ++++ metan-1.3.0/metan/R/ge_cluster.R | 30 metan-1.3.0/metan/R/ge_details.R | 14 metan-1.3.0/metan/R/ge_effects.R | 81 metan-1.3.0/metan/R/ge_factanal.R | 216 + metan-1.3.0/metan/R/ge_means.R | 6 metan-1.3.0/metan/R/ge_plot.R | 3 metan-1.3.0/metan/R/ge_reg.R | 173 + metan-1.3.0/metan/R/ge_stats.R | 83 metan-1.3.0/metan/R/ge_winners.R | 6 metan-1.3.0/metan/R/get_model_data.R | 592 ++-- metan-1.3.0/metan/R/gge.R | 798 ++++++ metan-1.3.0/metan/R/inspect.R | 2 metan-1.3.0/metan/R/is.lpcorr.R | 14 metan-1.3.0/metan/R/lpcorr.R | 87 metan-1.3.0/metan/R/mahala.R | 20 metan-1.3.0/metan/R/mahala_design.R | 144 - metan-1.3.0/metan/R/make_long.R | 7 metan-1.3.0/metan/R/make_mat.R | 10 metan-1.3.0/metan/R/pairs_mantel.R | 24 metan-1.3.0/metan/R/path_coeff.R | 976 +++----- metan-1.3.0/metan/R/performs_ammi.R | 364 ++ metan-1.3.0/metan/R/plot_blup.R | 8 metan-1.3.0/metan/R/plot_ci.R | 3 metan-1.3.0/metan/R/plot_factbars.R | 3 metan-1.3.0/metan/R/plot_scores.R | 309 +- metan-1.3.0/metan/R/rbind_fill.R | 7 metan-1.3.0/metan/R/remove_na_values.R | 2 metan-1.3.0/metan/R/resca.R | 3 metan-1.3.0/metan/R/resende_indexes.R | 24 metan-1.3.0/metan/R/residual_plots.R |only metan-1.3.0/metan/R/resp_surf.R | 64 metan-1.3.0/metan/R/select_helpers.R | 98 metan-1.3.0/metan/R/solve_svd.R | 4 metan-1.3.0/metan/R/split_factors.R | 73 metan-1.3.0/metan/R/superiority.R | 63 metan-1.3.0/metan/R/themes.R | 29 metan-1.3.0/metan/R/to_factor.R | 3 metan-1.3.0/metan/R/tukey_hsd.R |only metan-1.3.0/metan/R/utilities.R | 971 +++++++ metan-1.3.0/metan/R/waas.R | 366 ++- metan-1.3.0/metan/R/waas_means.R | 12 metan-1.3.0/metan/R/wsmp.R | 459 ++- metan-1.3.0/metan/R/zzz.R | 25 metan-1.3.0/metan/build/vignette.rds |binary metan-1.3.0/metan/inst/CITATION |only metan-1.3.0/metan/inst/doc/metan_start.R |only metan-1.3.0/metan/inst/doc/metan_start.Rmd |only metan-1.3.0/metan/inst/doc/metan_start.html |only metan-1.3.0/metan/man/Annicchiarico.Rd | 4 metan-1.3.0/metan/man/Fox.Rd | 3 metan-1.3.0/metan/man/Huehn.Rd | 3 metan-1.3.0/metan/man/Schmildt.Rd | 4 metan-1.3.0/metan/man/Select_helper.Rd | 69 metan-1.3.0/metan/man/Shukla.Rd | 4 metan-1.3.0/metan/man/Thennarasu.Rd | 3 metan-1.3.0/metan/man/anova_ind.Rd | 64 metan-1.3.0/metan/man/anova_joint.Rd | 57 metan-1.3.0/metan/man/arrange_ggplot.Rd | 2 metan-1.3.0/metan/man/as.lpcor.Rd | 4 metan-1.3.0/metan/man/can_corr.Rd | 49 metan-1.3.0/metan/man/clustering.Rd | 55 metan-1.3.0/metan/man/colindiag.Rd | 33 metan-1.3.0/metan/man/comb_vars.Rd | 4 metan-1.3.0/metan/man/corr_ci.Rd | 21 metan-1.3.0/metan/man/corr_coef.Rd | 2 metan-1.3.0/metan/man/corr_ss.Rd | 3 metan-1.3.0/metan/man/covcor_design.Rd | 24 metan-1.3.0/metan/man/cv_ammi.Rd | 6 metan-1.3.0/metan/man/cv_ammif.Rd | 6 metan-1.3.0/metan/man/cv_blup.Rd | 58 metan-1.3.0/metan/man/desc_stat.Rd | 177 - metan-1.3.0/metan/man/doo.Rd |only metan-1.3.0/metan/man/ecovalence.Rd | 3 metan-1.3.0/metan/man/env_dissimilarity.Rd | 2 metan-1.3.0/metan/man/figures/README-AMMI-1.png |binary metan-1.3.0/metan/man/figures/README-GGE-1.png |binary metan-1.3.0/metan/man/figures/README-unnamed-chunk-5-1.png |binary metan-1.3.0/metan/man/figures/logo.png |binary metan-1.3.0/metan/man/find_outliers.Rd | 10 metan-1.3.0/metan/man/gafem.Rd |only metan-1.3.0/metan/man/gai.Rd | 3 metan-1.3.0/metan/man/gamem.Rd | 54 metan-1.3.0/metan/man/ge_cluster.Rd | 5 metan-1.3.0/metan/man/ge_details.Rd | 4 metan-1.3.0/metan/man/ge_effects.Rd | 3 metan-1.3.0/metan/man/ge_factanal.Rd | 13 metan-1.3.0/metan/man/ge_plot.Rd | 3 metan-1.3.0/metan/man/get_model_data.Rd | 72 metan-1.3.0/metan/man/is.lpcor.Rd | 14 metan-1.3.0/metan/man/lpcor.Rd | 22 metan-1.3.0/metan/man/mahala.Rd | 20 metan-1.3.0/metan/man/mahala_design.Rd | 36 metan-1.3.0/metan/man/make_long.Rd | 3 metan-1.3.0/metan/man/make_mat.Rd | 8 metan-1.3.0/metan/man/pairs_mantel.Rd | 5 metan-1.3.0/metan/man/path_coeff.Rd | 42 metan-1.3.0/metan/man/performs_ammi.Rd | 45 metan-1.3.0/metan/man/plot.anova_joint.Rd |only metan-1.3.0/metan/man/plot.can_cor.Rd | 17 metan-1.3.0/metan/man/plot.clustering.Rd | 16 metan-1.3.0/metan/man/plot.corr_coef.Rd | 2 metan-1.3.0/metan/man/plot.cvalidation.Rd | 2 metan-1.3.0/metan/man/plot.env_dissimilarity.Rd | 3 metan-1.3.0/metan/man/plot.fai_blup.Rd | 2 metan-1.3.0/metan/man/plot.gafem.Rd |only metan-1.3.0/metan/man/plot.gamem.Rd |only metan-1.3.0/metan/man/plot.ge_cluster.Rd | 2 metan-1.3.0/metan/man/plot.ge_effects.Rd | 4 metan-1.3.0/metan/man/plot.ge_factanal.Rd | 5 metan-1.3.0/metan/man/plot.ge_reg.Rd | 4 metan-1.3.0/metan/man/plot.gge.Rd | 2 metan-1.3.0/metan/man/plot.mtsi.Rd | 2 metan-1.3.0/metan/man/plot.performs_ammi.Rd | 82 metan-1.3.0/metan/man/plot.resp_surf.Rd | 2 metan-1.3.0/metan/man/plot.waas.Rd | 82 metan-1.3.0/metan/man/plot.waasb.Rd | 2 metan-1.3.0/metan/man/plot.wsmp.Rd | 76 metan-1.3.0/metan/man/plot_ci.Rd | 3 metan-1.3.0/metan/man/plot_factbars.Rd | 3 metan-1.3.0/metan/man/plot_scores.Rd | 46 metan-1.3.0/metan/man/predict.gamem.Rd |only metan-1.3.0/metan/man/predict.gge.Rd | 5 metan-1.3.0/metan/man/predict.performs_ammi.Rd | 5 metan-1.3.0/metan/man/predict.waas.Rd | 10 metan-1.3.0/metan/man/predict.waasb.Rd |only metan-1.3.0/metan/man/print.AMMI_indexes.Rd | 5 metan-1.3.0/metan/man/print.Annicchiarico.Rd | 5 metan-1.3.0/metan/man/print.Fox.Rd | 15 metan-1.3.0/metan/man/print.Schmildt.Rd | 3 metan-1.3.0/metan/man/print.Shukla.Rd | 5 metan-1.3.0/metan/man/print.anova_ind.Rd | 5 metan-1.3.0/metan/man/print.anova_joint.Rd | 5 metan-1.3.0/metan/man/print.can_cor.Rd | 12 metan-1.3.0/metan/man/print.colindiag.Rd |only metan-1.3.0/metan/man/print.corr_coef.Rd | 3 metan-1.3.0/metan/man/print.ecovalence.Rd | 14 metan-1.3.0/metan/man/print.env_dissimilarity.Rd | 3 metan-1.3.0/metan/man/print.gamem.Rd | 5 metan-1.3.0/metan/man/print.ge_factanal.Rd | 5 metan-1.3.0/metan/man/print.ge_reg.Rd | 4 metan-1.3.0/metan/man/print.ge_stats.Rd | 2 metan-1.3.0/metan/man/print.mtsi.Rd | 4 metan-1.3.0/metan/man/print.path_coeff.Rd | 9 metan-1.3.0/metan/man/print.performs_ammi.Rd | 9 metan-1.3.0/metan/man/print.superiority.Rd | 5 metan-1.3.0/metan/man/print.waas.Rd | 2 metan-1.3.0/metan/man/print.waasb.Rd | 2 metan-1.3.0/metan/man/rbind_fill.Rd | 7 metan-1.3.0/metan/man/reexports.Rd | 7 metan-1.3.0/metan/man/remove_na_values.Rd | 2 metan-1.3.0/metan/man/reorder_cormat.Rd | 3 metan-1.3.0/metan/man/resca.Rd | 3 metan-1.3.0/metan/man/residual_plots.Rd |only metan-1.3.0/metan/man/resp_surf.Rd | 6 metan-1.3.0/metan/man/solve_svd.Rd | 4 metan-1.3.0/metan/man/split_factors.Rd | 45 metan-1.3.0/metan/man/stars_pval.Rd |only metan-1.3.0/metan/man/superiority.Rd | 4 metan-1.3.0/metan/man/themes.Rd | 15 metan-1.3.0/metan/man/to_factor.Rd | 3 metan-1.3.0/metan/man/tukey_hsd.Rd |only metan-1.3.0/metan/man/utils_class.Rd |only metan-1.3.0/metan/man/utils_mat.Rd |only metan-1.3.0/metan/man/utils_num_str.Rd | 104 metan-1.3.0/metan/man/utils_rows_cols.Rd | 29 metan-1.3.0/metan/man/utils_stats.Rd |only metan-1.3.0/metan/man/waas.Rd | 91 metan-1.3.0/metan/man/waas_means.Rd | 5 metan-1.3.0/metan/man/waasb.Rd | 252 +- metan-1.3.0/metan/man/wsmp.Rd | 61 metan-1.3.0/metan/vignettes/metan_start.Rmd |only metan-1.3.0/metan/vignettes/metanref.bib | 28 265 files changed, 10135 insertions(+), 5126 deletions(-)
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>
Diff between StanHeaders versions 2.21.0-1 dated 2020-01-19 and 2.19.2 dated 2020-02-11
StanHeaders-2.19.2/StanHeaders/DESCRIPTION | 15 StanHeaders-2.19.2/StanHeaders/MD5 | 3443 ++++------ StanHeaders-2.19.2/StanHeaders/NAMESPACE | 1 StanHeaders-2.19.2/StanHeaders/inst/CITATION | 6 StanHeaders-2.19.2/StanHeaders/inst/doc/stanmath.R | 15 StanHeaders-2.19.2/StanHeaders/inst/doc/stanmath.Rmd | 56 StanHeaders-2.19.2/StanHeaders/inst/doc/stanmath.html | 468 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_effective_sample_size.hpp | 292 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/callbacks/interrupt.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/callbacks/logger.hpp | 182 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/callbacks/stream_logger.hpp | 134 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/callbacks/stream_writer.hpp | 191 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/callbacks/tee_writer.hpp | 106 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/callbacks/writer.hpp | 86 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/command/stanc_helper.hpp | 221 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/array_var_context.hpp | 626 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/chained_var_context.hpp | 107 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/cmd_line.hpp | 519 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/dump.hpp | 1470 ++-- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/empty_var_context.hpp | 184 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/ends_with.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/is_whitespace.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/json |only StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/program_reader.hpp | 79 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/random_var_context.hpp | 479 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/read_line.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/reader.hpp | 139 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/stan_csv_reader.hpp | 667 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/starts_with.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/trim_spaces.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/util.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/validate_zero_buf.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/var_context.hpp | 485 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/io/writer.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_is_data_vis.hpp | 152 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_is_data_vis_def.hpp | 68 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_order_id_vis.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_order_id_vis_def.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_set_is_data_vis.hpp | 136 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_set_is_data_vis_def.hpp | 70 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_total_dims_vis.hpp | 138 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_total_dims_vis_def.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/bare_type_vis.hpp | 360 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_bounds_vis.hpp | 264 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_is_specialized_vis.hpp | 267 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/block_type_offset_multiplier_vis_def.hpp | 60 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/ends_with.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/ends_with_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/fun_name_exists.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/fun_name_exists_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/generate_expression.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/get_ccdf.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/get_ccdf_def.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/get_cdf.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/get_cdf_def.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/get_prob_fun.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/get_prob_fun_def.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_ccdf_suffix.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_ccdf_suffix_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_cdf_suffix.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_cdf_suffix_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_lp_suffix.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_lp_suffix_def.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_def.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis.hpp | 386 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_non_param_var_vis_def.hpp | 296 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_prob_fun_suffix.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_prob_fun_suffix_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_rng_suffix.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_rng_suffix_def.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis.hpp | 418 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/has_var_vis_def.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/infer_type_indexing.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/infer_type_indexing_def.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable.hpp | 43 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_assignable_def.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index_vis.hpp | 110 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_multi_index_vis_def.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis.hpp | 94 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nil_vis_def.hpp | 98 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_no_op_statement_vis.hpp | 304 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_no_op_statement_vis_def.hpp | 134 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nonempty.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_nonempty_def.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_space.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_space_def.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined_def.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined_prob_function.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/is_user_defined_prob_function_def.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/num_index_op_dims.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/print_scope.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/print_scope_def.hpp | 66 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive.hpp | 58 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/promote_primitive_def.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis.hpp | 415 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/returns_type_vis_def.hpp | 208 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_ccdf_suffix.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_cdf_suffix.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/strip_prob_fun_suffix.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/template.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis.hpp | 428 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/var_occurs_vis_def.hpp | 186 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg1_vis.hpp | 362 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg1_vis_def.hpp | 219 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg2_vis.hpp | 367 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/var_type_arg2_vis_def.hpp | 219 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/write_bare_expr_type.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/write_bare_expr_type_def.hpp | 61 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/write_block_var_type.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/fun/write_idx_vis_def.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/nil.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver.hpp | 104 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver_control.hpp | 149 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver_control_def.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/algebra_solver_def.hpp | 23 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/assgn.hpp | 155 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/assgn_def.hpp | 41 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/binary_op.hpp | 88 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/binary_op_def.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/block_var_decl_def.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/break_continue_statement.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/break_continue_statement_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_op.hpp | 113 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_op_def.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_statement.hpp | 66 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/conditional_statement_def.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/distribution.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/expression.hpp | 151 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/expression_def.hpp | 104 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/for_array_statement.hpp | 77 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/for_array_statement_def.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/for_matrix_statement.hpp | 77 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/for_matrix_statement_def.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/for_statement.hpp | 76 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/for_statement_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/fun.hpp | 91 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/fun_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_def.hpp | 109 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_def_def.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_defs.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/function_decl_defs_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/idx.hpp | 143 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/idx_def.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/increment_log_prob_statement.hpp | 54 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/increment_log_prob_statement_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/index_op.hpp | 85 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/index_op_sliced.hpp | 87 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/index_op_sliced_def.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/int_literal.hpp | 52 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/int_literal_def.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_1d.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_1d_def.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode.hpp | 145 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode_control.hpp | 190 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode_control_def.hpp | 38 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/integrate_ode_def.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/lb_idx.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/lb_idx_def.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/local_var_decl_def.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/lub_idx.hpp | 63 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/lub_idx_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/map_rect.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/map_rect_def.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/matrix_expr.hpp | 78 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/matrix_expr_def.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/multi_idx.hpp | 38 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/multi_idx_def.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/no_op_statement.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/omni_idx.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/omni_idx_def.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/print_statement.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/print_statement_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/printable.hpp | 104 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/printable_def.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/program.hpp | 177 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/program_def.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/range.hpp | 92 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/range_def.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/reject_statement.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/reject_statement_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/return_statement.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/return_statement_def.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_expr.hpp | 78 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/row_vector_expr_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/sample.hpp | 111 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/sample_def.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/statement.hpp | 414 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/statement_def.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/statements.hpp | 70 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/statements_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/ub_idx.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/ub_idx_def.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/unary_op.hpp | 74 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/unary_op_def.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/uni_idx.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/uni_idx_def.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/var_decl.hpp | 152 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/var_decl_def.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/variable.hpp | 72 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/variable_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/variable_dims.hpp | 65 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/variable_dims_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/while_statement.hpp | 65 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/node/while_statement_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/origin_block.hpp | 160 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/scope.hpp | 294 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/scope_def.hpp | 173 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signature_t.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures.hpp | 813 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/sigs/function_signatures_def.hpp | 921 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/bare_array_type_def.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/block_array_type_def.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/cholesky_factor_corr_block_type.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/cholesky_factor_cov_block_type.hpp | 87 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/double_block_type_def.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/double_type.hpp | 58 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/double_type_def.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/ill_formed_type.hpp | 47 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/ill_formed_type_def.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/int_block_type_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/int_type.hpp | 59 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/int_type_def.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/local_array_type_def.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/local_var_type.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/local_var_type_def.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_block_type_def.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_local_type.hpp | 83 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_type.hpp | 58 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/matrix_type_def.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_block_type_def.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_local_type_def.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_type.hpp | 58 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/row_vector_type_def.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/vector_block_type_def.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/vector_type.hpp | 58 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/vector_type_def.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/void_type.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/type/void_type_def.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/variable_map.hpp | 167 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/ast/variable_map_def.hpp | 65 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/compile_functions.hpp | 83 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/compiler.hpp | 75 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/function_signatures.h | 139 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/constants.hpp | 84 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/expression_visgen.hpp | 603 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/fun_scalar_type.hpp | 90 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_arg_decl.hpp | 50 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_array_builder_adds.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_bare_type.hpp | 99 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_block_var.hpp | 89 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_catch_throw_located.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_class_decl.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_class_decl_end.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_comment.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_constrained_param_names_method.hpp | 65 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_constructor.hpp | 217 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_cpp.hpp | 88 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_data_var_ctor.hpp | 52 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_data_var_init.hpp | 85 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_destructor.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_dims_method.hpp | 94 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_expression.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_fun_inst_templ_params.hpp | 103 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function.hpp | 71 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_arguments.hpp | 118 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_body.hpp | 75 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_functor.hpp | 83 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_inline_return_type.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation.hpp | 86 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation_body.hpp | 110 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiation_name.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_instantiations.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_name.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_function_template_parameters.hpp | 106 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_functions.hpp | 38 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_functor_arguments.hpp | 68 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_globals.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_idx.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_idx_user.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_idxs.hpp | 65 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_idxs_user.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_include.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_includes.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_indent.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_indexed_expr.hpp | 128 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_indexed_expr_user.hpp | 54 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_initializer.hpp | 87 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_line_number.hpp | 41 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_local_var_decl_inits.hpp | 122 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_log_prob.hpp | 204 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_member_var_decls.hpp | 64 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_member_var_decls_all.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_model_name_method.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_model_typedef.hpp | 38 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_namespace_end.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_namespace_start.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_param_names_array.hpp | 77 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_param_names_method.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_param_var.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_printable.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_private_decl.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_program_reader_fun.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_propto_default_function.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_propto_default_function_body.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_public_decl.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_quoted_expression.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_quoted_string.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_read_transform_params.hpp | 101 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_real_var_type.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_register_mpi.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_set_param_ranges.hpp | 89 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_standalone_functions.hpp | 82 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_statement.hpp | 43 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_statements.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_transform_inits_method.hpp | 302 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_try.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_typedef.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_typedefs.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_array.hpp | 80 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_unconstrained_param_names_method.hpp | 68 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_using.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_using_namespace.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_usings.hpp | 38 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_usings_standalone_functions.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_block_var.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_context_size.hpp | 82 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_nonnegative.hpp | 62 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_tparam_inits.hpp | 93 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_var_decl.hpp | 116 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_validate_var_dims.hpp | 69 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_var_constructor.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_var_fill_define.hpp | 61 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_version_comment.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_void_statement.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_write_array_method.hpp | 283 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/generate_write_block_var.hpp | 41 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/get_block_var_dims.hpp | 55 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/get_typedef_var_type.hpp | 41 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/get_verbose_var_type.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/idx_user_visgen.hpp | 82 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/idx_visgen.hpp | 92 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/is_numbered_statement_vis.hpp | 68 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/printable_visgen.hpp | 64 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/statement_visgen.hpp | 699 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/visgen.hpp | 100 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_begin_all_dims_col_maj_loop.hpp | 139 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_begin_all_dims_row_maj_loop.hpp | 139 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_begin_array_dims_loop.hpp | 68 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_begin_param_elements_loop.hpp | 147 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_constraints_fn.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_end_loop.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_nested_resize_loop_begin.hpp | 108 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_resize_var_idx.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_var_decl_arg.hpp | 130 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_var_decl_type.hpp | 70 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_all_dims.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_all_dims_msg.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/generator/write_var_idx_array_dims.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar.hpp | 54 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar_def.hpp | 93 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/bare_type_grammar_inst.cpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/block_var_decls_grammar_def.hpp | 284 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/block_var_decls_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/common_adaptors_def.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/expression07_grammar.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/expression07_grammar_def.hpp | 58 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/expression07_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar.hpp | 70 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar_def.hpp | 157 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/expression_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar.hpp | 72 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_def.hpp | 167 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/functions_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar.hpp | 91 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar_def.hpp | 158 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/indexes_grammar_inst.cpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/iterator_typedefs.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar.hpp | 115 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar_def.hpp | 248 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/local_var_decls_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar.hpp | 110 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar_def.hpp | 252 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/program_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/semantic_actions_def.cpp | 439 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar.hpp | 52 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar_def.hpp | 92 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/statement_2_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar.hpp | 190 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_def.hpp | 612 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/statement_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar.hpp | 169 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_def.hpp | 654 + StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/term_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar_def.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/var_decls_grammar_inst.cpp |only StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/whitespace_grammar.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/whitespace_grammar_def.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/grammars/whitespace_grammar_inst.cpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/parser.hpp | 186 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/lang/rethrow_located.hpp | 284 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/base_adaptation.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/base_adapter.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/base_mcmc.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/chains.hpp | 1052 +-- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/covar_adaptation.hpp | 54 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/fixed_param_sampler.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/base_hmc.hpp | 337 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/base_hamiltonian.hpp | 173 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_metric.hpp | 97 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/dense_e_point.hpp | 113 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/diag_e_metric.hpp | 88 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/diag_e_point.hpp | 108 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/ps_point.hpp | 134 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/softabs_metric.hpp | 354 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/softabs_point.hpp | 55 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/unit_e_metric.hpp | 85 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/hamiltonians/unit_e_point.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/base_integrator.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/base_leapfrog.hpp | 228 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/expl_leapfrog.hpp | 50 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/integrators/impl_leapfrog.hpp | 173 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_dense_e_nuts.hpp | 79 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_diag_e_nuts.hpp | 79 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_softabs_nuts.hpp | 66 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/adapt_unit_e_nuts.hpp | 66 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/base_nuts.hpp | 626 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/dense_e_nuts.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/diag_e_nuts.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/softabs_nuts.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts/unit_e_nuts.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_dense_e_nuts_classic.hpp | 84 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_diag_e_nuts_classic.hpp | 86 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/adapt_unit_e_nuts_classic.hpp | 67 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/base_nuts_classic.hpp | 368 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/dense_e_nuts_classic.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/diag_e_nuts_classic.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/nuts_classic/unit_e_nuts_classic.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_dense_e_static_hmc.hpp | 92 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_diag_e_static_hmc.hpp | 87 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_softabs_static_hmc.hpp | 72 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/adapt_unit_e_static_hmc.hpp | 74 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/base_static_hmc.hpp | 237 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/dense_e_static_hmc.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/diag_e_static_hmc.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/softabs_static_hmc.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static/unit_e_static_hmc.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_dense_e_static_uniform.hpp | 88 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_diag_e_static_uniform.hpp | 87 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_softabs_static_uniform.hpp | 63 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/adapt_unit_e_static_uniform.hpp | 74 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/base_static_uniform.hpp | 281 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/dense_e_static_uniform.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/diag_e_static_uniform.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/softabs_static_uniform.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/static_uniform/unit_e_static_uniform.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_dense_e_xhmc.hpp | 85 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_diag_e_xhmc.hpp | 85 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_softabs_xhmc.hpp | 66 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/adapt_unit_e_xhmc.hpp | 67 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/base_xhmc.hpp | 522 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/dense_e_xhmc.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/diag_e_xhmc.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/softabs_xhmc.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/hmc/xhmc/unit_e_xhmc.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/sample.hpp | 83 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/stepsize_adaptation.hpp | 169 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/stepsize_adapter.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/stepsize_covar_adapter.hpp | 57 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/stepsize_var_adapter.hpp | 58 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/var_adaptation.hpp | 52 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/mcmc/windowed_adaptation.hpp | 231 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/finite_diff_grad.hpp | 95 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/grad_hess_log_prob.hpp | 120 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/grad_tr_mat_times_hessian.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/gradient.hpp | 50 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/gradient_dot_vector.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/hessian.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/hessian_times_vector.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/deep_copy.hpp | 112 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/index.hpp | 193 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/index_list.hpp | 123 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/lvalue.hpp | 877 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/rvalue.hpp | 700 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/rvalue_at.hpp | 130 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/rvalue_index_size.hpp | 118 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/indexing/rvalue_return.hpp | 410 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/log_prob_grad.hpp | 165 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/log_prob_propto.hpp | 178 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/model_functional.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/model_header.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/prob_grad.hpp | 113 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/standalone_functions_header.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/model/test_gradients.hpp | 174 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/optimization/bfgs.hpp | 785 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/optimization/bfgs_linesearch.hpp | 547 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/optimization/bfgs_update.hpp | 111 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/optimization/lbfgs_update.hpp | 206 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/optimization/newton.hpp | 124 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/diagnose/defaults.hpp | 137 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/diagnose/diagnose.hpp | 100 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/error_codes.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/experimental/advi/defaults.hpp | 630 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/experimental/advi/fullrank.hpp | 152 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/experimental/advi/meanfield.hpp | 152 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/optimize/bfgs.hpp | 325 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/optimize/defaults.hpp | 624 - StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/optimize/lbfgs.hpp | 329 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/optimize/newton.hpp | 207 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/defaults.hpp | 969 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/fixed_param.hpp | 130 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e.hpp | 241 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_dense_e_adapt.hpp | 299 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e.hpp | 239 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_diag_e_adapt.hpp | 295 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e.hpp | 116 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_nuts_unit_e_adapt.hpp | 138 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e.hpp | 238 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_static_dense_e_adapt.hpp | 300 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e.hpp | 238 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_static_diag_e_adapt.hpp | 298 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e.hpp | 115 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/hmc_static_unit_e_adapt.hpp | 139 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/sample/standalone_gqs.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/create_rng.hpp | 55 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/create_unit_e_dense_inv_metric.hpp | 54 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/create_unit_e_diag_inv_metric.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/experimental_message.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/generate_transitions.hpp | 127 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/gq_writer.hpp | 165 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/initialize.hpp | 95 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/mcmc_writer.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/read_dense_inv_metric.hpp | 67 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/read_diag_inv_metric.hpp | 68 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/run_adaptive_sampler.hpp | 157 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/run_sampler.hpp | 130 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/validate_dense_inv_metric.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/services/util/validate_diag_inv_metric.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/variational/advi.hpp | 1043 +-- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/variational/base_family.hpp | 196 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/variational/families/normal_fullrank.hpp | 970 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/variational/families/normal_meanfield.hpp | 848 +- StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/variational/print_progress.hpp | 87 StanHeaders-2.19.2/StanHeaders/inst/include/src/stan/version.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/arr.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/arr/fun/log_sum_exp.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/arr/fun/sum.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/arr/fun/to_fvar.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/core/fvar.hpp | 43 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/Eigen_NumTraits.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/columns_dot_product.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/columns_dot_self.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/crossprod.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/determinant.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/divide.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/dot_product.hpp | 38 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/dot_self.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/inverse.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_determinant.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_softmax.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/log_sum_exp.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left_ldlt.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_left_tri_low.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_right.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/mdivide_right_tri_low.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/multiply.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/multiply_lower_tri_self_transpose.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/qr_Q.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/qr_R.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/quad_form_sym.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/rows_dot_product.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/rows_dot_self.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/softmax.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/squared_distance.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/sum.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/tcrossprod.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/to_fvar.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/typedefs.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/fun/unit_vector_constrain.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/functor/gradient.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/functor/hessian.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/functor/jacobian.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/meta/operands_and_partials.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/mat/vectorize/apply_scalar_unary.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/Phi.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/Phi_approx.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/abs.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/acos.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/acosh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/asin.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/asinh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/atan.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/atan2.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/atanh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/bessel_first_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/bessel_second_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/binary_log_loss.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/binomial_coefficient_log.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/cbrt.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/ceil.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/cos.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/cosh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/digamma.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/erf.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/erfc.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/exp.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/exp2.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/expm1.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/fabs.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/falling_factorial.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/fdim.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/floor.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/fma.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmax.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmin.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/fmod.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_p.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/gamma_q.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/grad_inc_beta.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/hypot.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/inc_beta.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_Phi.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_cloglog.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_logit.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_sqrt.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/inv_square.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/is_inf.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/is_nan.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/lbeta.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/lgamma.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/lmgamma.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log10.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m_exp.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1m_inv_logit.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1p.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log1p_exp.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log2.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_diff_exp.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_falling_factorial.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_inv_logit.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_inv_logit_diff.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_mix.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_rising_factorial.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/log_sum_exp.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/logit.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/modified_bessel_first_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/modified_bessel_second_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/multiply_log.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/owens_t.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/pow.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/primitive_value.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/rising_factorial.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/round.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/sin.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/sinh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/sqrt.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/square.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/tan.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/tanh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/tgamma.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/to_fvar.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/trigamma.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/trunc.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/value_of.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/fun/value_of_rec.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/meta/ad_promotable.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/meta/is_fvar.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/meta/operands_and_partials.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/fwd/scal/meta/partials_type.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/memory/stack_alloc.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/arr.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/fun/typedefs.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/functor/finite_diff_grad_hessian.hpp | 23 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_hessian.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/functor/grad_tr_mat_times_hessian.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/functor/gradient_dot_vector.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/functor/hessian_times_vector.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/mat/functor/partial_derivative.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/mix/scal.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/add.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/cholesky_decompose.hpp | 89 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/constants.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/copy.hpp | 256 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/copy_triangular.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/diagonal_multiply.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/err/check_diagonal_zeros.hpp | 23 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/err/check_matching_dims.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/err/check_nan.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/err/check_square.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/err/check_symmetric.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/identity.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernel_cl.hpp | 321 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/add.hpp | 75 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/check_diagonal_zeros.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/check_nan.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/check_symmetric.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/cholesky_decompose.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/copy.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/copy_triangular.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/diag_inv.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/helpers.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/identity.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/inv_lower_tri_multiply.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/matrix_multiply.hpp | 323 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/multiply_transpose.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/neg_rect_lower_tri_multiply.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/pack.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/scalar_mul.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/scalar_mul_diagonal.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/sub_block.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/subtract.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/transpose.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/triangular_transpose.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/unpack.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/kernels/zeros.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/lower_tri_inverse.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/matrix_cl.hpp | 536 - StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/multiply.hpp | 135 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/multiply_transpose.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/opencl_context.hpp | 83 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/subtract.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/opencl/transpose.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/check_matching_sizes.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/check_nonzero_size.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/check_opencl.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/check_ordered.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/is_matching_size.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/is_nonzero_size.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/err/is_ordered.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/array_builder.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/common_type.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/dot.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/dot_self.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/fill.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/inverse_softmax.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/log_sum_exp.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_elements.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/promote_scalar_type.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/rep_array.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/scaled_add.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_asc.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/sort_desc.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/sub.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/sum.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/fun/value_of_rec.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/functor/coupled_ode_observer.hpp | 136 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/functor/coupled_ode_system.hpp | 98 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/functor/integrate_1d.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/functor/integrate_ode_rk45.hpp | 77 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/VectorBuilderHelper.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/contains_std_vector.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/index_type.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/is_constant_struct.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/is_vector.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/scalar_type.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/arr/meta/value_type.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_cholesky_factor_corr.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_column_index.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_size_mvt.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_consistent_sizes_mvt.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_corr_matrix.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_cov_matrix.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_finite.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_ldlt_factor.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_lower_triangular.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_matching_dims.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_multiplicable.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_ordered.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_definite.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_pos_semidefinite.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_positive_ordered.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_range.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_row_index.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_simplex.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_spsd_matrix.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_square.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_std_vector_index.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_symmetric.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_unit_vector.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/check_vector.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/constraint_tolerance.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_cholesky_factor_corr.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_column_index.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_corr_matrix.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_ldlt_factor.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_lower_triangular.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_mat_finite.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_matching_dims.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_pos_definite.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_square.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_symmetric.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/is_unit_vector.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/err/validate_non_negative_index.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/Eigen.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/LDLT_factor.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/MatrixExponential.h | 31 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/accumulator.hpp | 23 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/add.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/add_diag.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/append_array.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/append_col.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/append_row.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/assign.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/autocorrelation.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/chol2inv.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_constrain.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_corr_free.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_decompose.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_constrain.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cholesky_factor_free.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/common_type.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_constrain.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/corr_matrix_free.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_exp_quad.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_constrain_lkj.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cov_matrix_free_lkj.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_u.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_v.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_extract_w.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_matrix_times_vector.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/csr_to_dense_matrix.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/cumulative_sum.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_post_multiply.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/diag_pre_multiply.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/digamma.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/dims.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/distance.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/divide.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/divide_columns.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/dot_product.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_divide.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/elt_multiply.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/exp2.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_U.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/factor_cov_matrix.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/get_lp.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_dot_prod_cov.hpp | 38 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exp_quad_cov.hpp | 588 - StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_exponential_cov.hpp | 89 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern32_cov.hpp | 99 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_matern52_cov.hpp | 138 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/gp_periodic_cov.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/head.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/initialize.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/inverse_spd.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/log2.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/log_mix.hpp | 126 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/log_sum_exp.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/make_nu.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_2x2.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_action_handler.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/matrix_exp_pade.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/max.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_ldlt.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_spd.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri.hpp | 99 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_left_tri_low.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_ldlt.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_spd.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri.hpp | 47 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mdivide_right_tri_low.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/mean.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/min.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply.hpp | 60 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/multiply_lower_tri_self_transpose.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/num_elements.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_constrain.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/ordered_free.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_constrain.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/positive_ordered_free.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/prod.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_elements.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/promote_scalar_type.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_Q.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_R.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_Q.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/qr_thin_R.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/quad_form_diag.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/rank.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/read_corr_L.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_matrix.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_row_vector.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/rep_vector.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/resize.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/sd.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/segment.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/simplex_constrain.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/simplex_free.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices_asc.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/sort_indices_desc.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/stan_print.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/sub_col.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/sub_row.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/subtract.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/tail.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/tcrossprod.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_1d.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/to_array_2d.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/to_matrix.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/to_row_vector.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/to_vector.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_inv_quad_form_ldlt.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_gen_quad_form.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/trace_inv_quad_form_ldlt.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/typedefs.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_constrain.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/unit_vector_free.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/value_of_rec.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/variance.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/welford_covar_estimator.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/fun/welford_var_estimator.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_gradient.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_hessian.hpp | 83 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_combine.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_concurrent.hpp | 130 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_mpi.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/map_rect_reduce.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/functor/mpi_parallel_call.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/append_return_type.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/as_array_or_scalar.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/as_column_vector_or_scalar.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/as_scalar.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/broadcast_array.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/index_type.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/is_constant_struct.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/is_vector.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/is_vector_like.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/operands_and_partials.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/scalar_type.hpp | 59 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/seq_view.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/meta/value_type.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_lpmf.hpp | 73 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_log.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_lpmf.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_lpmf.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_rng.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_lpmf.hpp | 103 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/dirichlet_rng.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_log.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_lpdf.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_lpdf.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/inv_wishart_rng.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_lpdf.hpp | 59 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_cholesky_rng.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_lpdf.hpp | 83 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_corr_rng.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_cov_log.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/lkj_cov_lpdf.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_lpdf.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_cholesky_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_cholesky_lpdf.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_gp_lpdf.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_log.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_lpdf.hpp | 70 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_cholesky_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_lpdf.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_lpdf.hpp | 47 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_lpdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_student_t_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_log.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_lpmf.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/multinomial_rng.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/neg_binomial_2_log_glm_log.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/neg_binomial_2_log_glm_lpmf.hpp | 103 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/normal_id_glm_log.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/normal_id_glm_lpdf.hpp | 137 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_lpmf.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_rng.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_log.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_lpmf.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_probit_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/poisson_log_glm_log.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/poisson_log_glm_lpmf.hpp | 65 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_log.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_lpdf.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/prob/wishart_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/mat/vectorize/apply_scalar_unary.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal.hpp | 41 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_2F1_converges.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_3F2_converges.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_bounded.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_size.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_consistent_sizes.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_finite.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_greater_or_equal.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_less.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_less_or_equal.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_nonnegative.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_not_nan.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_positive_finite.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/check_size_match.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/domain_error_vec.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/invalid_argument_vec.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/is_less_or_equal.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/is_not_nan.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/is_positive.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/is_scal_finite.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/is_size_match.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/out_of_range.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/err/system_error.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/F32.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/Phi_approx.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/abs.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/acosh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/as_bool.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/asinh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/atanh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/bessel_first_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/bessel_second_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/binary_log_loss.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/binomial_coefficient_log.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/boost_policy.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/cbrt.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/choose.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/common_type.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/constants.hpp | 57 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/corr_constrain.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/corr_free.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/digamma.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/distance.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/divide.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/erf.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/erfc.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/exp.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/exp2.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/expm1.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/falling_factorial.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/fdim.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/fill.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/fma.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/fmax.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/fmin.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_p.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/gamma_q.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_2F1.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_F32.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_inc_beta.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_inc_beta.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_inc_gamma.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/grad_reg_lower_inc_gamma.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/hypot.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/ibeta.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/identity_constrain.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/identity_free.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/if_else.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_dda.hpp | 43 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_ddb.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inc_beta_ddz.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/int_step.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inv.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_Phi.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_cloglog.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_logit.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_sqrt.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/inv_square.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/is_inf.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/is_integer.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/is_nan.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/is_nonpositive_integer.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/is_uninitialized.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/lb_constrain.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/lb_free.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/lbeta.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/ldexp.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/lgamma.hpp | 67 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/lmgamma.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/locscale_constrain.hpp | 23 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/locscale_free.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m_exp.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log1m_inv_logit.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log1p_exp.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log2.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_diff_exp.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_falling_factorial.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_inv_logit.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_inv_logit_diff.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_mix.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_modified_bessel_first_kind.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_rising_factorial.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/log_sum_exp.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_and.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_eq.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_gt.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_gte.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_lt.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_lte.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_negation.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_neq.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logical_or.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/logit.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/lub_constrain.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/lub_free.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/modified_bessel_first_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/modified_bessel_second_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/modulus.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/multiply_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/offset_multiplier_constrain.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/offset_multiplier_free.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/owens_t.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/positive_constrain.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/positive_free.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/primitive_value.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/prob_constrain.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/prob_free.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_elements.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_scalar.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/promote_scalar_type.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/rising_factorial.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/round.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/sign.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/size_zero.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/sqrt.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/square.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/squared_distance.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/step.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/sum.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/tgamma.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/trigamma.hpp | 23 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/trunc.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/ub_constrain.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/ub_free.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/value_of.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/fun/value_of_rec.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/StdVectorBuilder.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/VectorBuilder.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/VectorBuilderHelper.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/ad_promotable.hpp | 146 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/child_type.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/conjunction.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_fvar.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_nonconstant_struct.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_std_vector.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/contains_vector.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/disjunction.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/include_summand.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/index_type.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_constant_struct.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_fvar.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_nonconstant_struct.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_var_or_arithmetic.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_vector.hpp | 77 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/is_vector_like.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/operands_and_partials.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/partials_return_type.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/partials_type.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/return_type.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_seq_view.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_type.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/scalar_type_pre.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/seq_view.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/meta/value_type.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_ccdf_log.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_cdf.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_cdf_log.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lccdf.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lcdf.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_lpmf.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_logit_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_lpmf.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/bernoulli_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_ccdf_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_cdf.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_cdf_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lccdf.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lcdf.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_lpmf.hpp | 140 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_binomial_rng.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf.hpp | 64 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lccdf.hpp | 50 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lcdf.hpp | 50 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_lpdf.hpp | 95 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lccdf.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lcdf.hpp | 52 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_lpdf.hpp | 71 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_proportion_rng.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/beta_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_ccdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_cdf.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_cdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lccdf.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lcdf.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_logit_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_logit_lpmf.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_lpmf.hpp | 50 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/binomial_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_cdf.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_cdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lccdf.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lcdf.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_lpdf.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/cauchy_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_ccdf_log.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_cdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_cdf_log.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lccdf.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lcdf.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_lpdf.hpp | 74 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/chi_square_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_cdf.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lccdf.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lcdf.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_lpdf.hpp | 56 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/double_exponential_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_ccdf_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_cdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_cdf_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lccdf.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lcdf.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_log.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_lpdf.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exp_mod_normal_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_ccdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_cdf.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_cdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lccdf.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lcdf.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_lpdf.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/exponential_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_cdf.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lccdf.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lcdf.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_lpdf.hpp | 85 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/frechet_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_cdf.hpp | 56 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lccdf.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lcdf.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_lpdf.hpp | 69 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gamma_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_cdf.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_cdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lccdf.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lcdf.hpp | 31 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_lpdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/gumbel_rng.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_log.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_lpmf.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/hypergeometric_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_ccdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_cdf.hpp | 53 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_cdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lccdf.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lcdf.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_lpdf.hpp | 73 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_chi_square_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_cdf.hpp | 65 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lccdf.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lcdf.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_lpdf.hpp | 86 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/inv_gamma_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_cdf.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lccdf.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lcdf.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_lpdf.hpp | 72 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/logistic_rng.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_cdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lccdf.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lcdf.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_lpdf.hpp | 88 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/lognormal_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_cdf.hpp | 44 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lccdf.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lcdf.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_lpmf.hpp | 63 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_log_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_lpmf.hpp | 67 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_2_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_cdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lccdf.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lcdf.hpp | 49 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_lpmf.hpp | 93 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/neg_binomial_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_cdf.hpp | 55 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lccdf.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lcdf.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_lpdf.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_sufficient_log.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/normal_sufficient_lpdf.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_cdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lccdf.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lcdf.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_lpdf.hpp | 81 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_cdf.hpp | 66 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lccdf.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lcdf.hpp | 37 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_log.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_lpdf.hpp | 68 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/pareto_type_2_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_ccdf_log.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_cdf.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_cdf_log.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lccdf.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lcdf.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_log.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_lpmf.hpp | 56 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_log_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_lpmf.hpp | 46 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/poisson_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_ccdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_cdf.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_cdf_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lccdf.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lcdf.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_lpdf.hpp | 45 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/rayleigh_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_cdf.hpp | 59 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lccdf.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lcdf.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_lpdf.hpp | 93 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/scaled_inv_chi_square_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_cdf.hpp | 50 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lccdf.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lcdf.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_lpdf.hpp | 56 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/skew_normal_rng.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/std_normal_log.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/std_normal_lpdf.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_ccdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_cdf.hpp | 85 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_cdf_log.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lccdf.hpp | 60 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lcdf.hpp | 64 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_log.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_lpdf.hpp | 78 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/student_t_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_cdf.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lccdf.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lcdf.hpp | 34 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_lpdf.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/uniform_rng.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_log.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_lpdf.hpp | 60 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/von_mises_rng.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_ccdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_cdf.hpp | 51 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_cdf_log.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lccdf.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lcdf.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_log.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_lpdf.hpp | 91 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/weibull_rng.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_log.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/prim/scal/prob/wiener_lpdf.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/arr.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/arr/fun/log_sum_exp.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/arr/fun/sum.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/arr/fun/to_var.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/arr/functor/coupled_ode_system.hpp | 509 - StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/arr/functor/integrate_1d.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/autodiffstackstorage.hpp | 136 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/build_vari_array.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/chainable_alloc.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/chainablestack.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/empty_nested.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/gevv_vvv_vari.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/grad.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/matrix_vari.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/nested_size.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_addition.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_divide_equal.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_division.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_minus_equal.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_multiplication.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_multiply_equal.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_plus_equal.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_subtraction.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_unary_decrement.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_unary_increment.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_unary_negative.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/operator_unary_plus.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/precomputed_gradients.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/print_stack.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/recover_memory.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/recover_memory_nested.hpp | 29 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/set_zero_all_adjoints_nested.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/start_nested.hpp | 14 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/stored_gradient_vari.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/var.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/vari.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/core/vector_vari.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/Eigen_NumTraits.hpp | 185 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/LDLT_alloc.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/LDLT_factor.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/cholesky_decompose.hpp | 79 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_product.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/columns_dot_self.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/cov_exp_quad.hpp | 43 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/crossprod.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/determinant.hpp | 40 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/divide.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_product.hpp | 100 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/dot_self.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/gp_exp_quad_cov.hpp | 56 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/gp_periodic_cov.hpp | 35 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/grad.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/initialize_variable.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant.hpp | 25 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant_ldlt.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/log_determinant_spd.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/log_softmax.hpp | 62 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/log_sum_exp.hpp | 26 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/matrix_exp_multiply.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left.hpp | 225 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_ldlt.hpp | 133 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_spd.hpp | 182 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/mdivide_left_tri.hpp | 354 - StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply.hpp | 371 - StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/multiply_lower_tri_self_transpose.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/ordered_constrain.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/positive_ordered_constrain.hpp | 7 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form.hpp | 23 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/quad_form_sym.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/rows_dot_product.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/scale_matrix_exp_multiply.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/sd.hpp | 48 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/simplex_constrain.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/softmax.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/squared_distance.hpp | 69 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/stan_print.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/sum.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/tcrossprod.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/to_var.hpp | 75 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_inv_quad_form_ldlt.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_gen_quad_form.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_inv_quad_form_ldlt.hpp | 78 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/trace_quad_form.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/typedefs.hpp | 27 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/unit_vector_constrain.hpp | 28 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/fun/variance.hpp | 39 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/adj_jac_apply.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_system.hpp | 33 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_integrator.hpp | 92 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_ode_data.hpp | 32 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/cvodes_utils.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/gradient.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_forward_system.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_integrator.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/idas_system.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_dae.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_ode_adams.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/integrate_ode_bdf.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/jacobian.hpp | 21 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/functor/map_rect_reduce.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/meta/operands_and_partials.hpp | 30 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/mat/vectorize/apply_scalar_unary.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/Phi.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/Phi_approx.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/abs.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/acos.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/acosh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/as_bool.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/asin.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/asinh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/atan.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/atan2.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/atanh.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_first_kind.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/bessel_second_kind.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/binary_log_loss.hpp | 8 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_fpclassify.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isfinite.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/boost_isnormal.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/calculate_chain.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/cbrt.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/ceil.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/cos.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/cosh.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/digamma.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/erf.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/erfc.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/exp.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/exp2.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/expm1.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/fabs.hpp | 10 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/falling_factorial.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/fdim.hpp | 16 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/floor.hpp | 5 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/fma.hpp | 42 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/fmax.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/fmin.hpp | 20 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/fmod.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_p.hpp | 13 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/gamma_q.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/grad_inc_beta.hpp | 9 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/hypot.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/ibeta.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/if_else.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/inc_beta.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/inv.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_Phi.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_cloglog.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_logit.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_sqrt.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/inv_square.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/is_inf.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/is_nan.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/is_uninitialized.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/lgamma.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/lmgamma.hpp | 6 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log10.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_exp.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log1m_inv_logit.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log1p_exp.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log2.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log_diff_exp.hpp | 24 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log_falling_factorial.hpp | 15 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log_inv_logit.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log_inv_logit_diff.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log_mix.hpp | 17 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log_rising_factorial.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/log_sum_exp.hpp | 18 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/logit.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_first_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/modified_bessel_second_kind.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/multiply_log.hpp | 22 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/owens_t.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/pow.hpp | 36 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/primitive_value.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/rising_factorial.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/round.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/sin.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/sinh.hpp | 2 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/sqrt.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/square.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/squared_distance.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/step.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/tan.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/tanh.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/tgamma.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/to_var.hpp | 19 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/trigamma.hpp | 3 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/trunc.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/value_of.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/fun/value_of_rec.hpp | 1 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/meta/ad_promotable.hpp |only StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/meta/is_var.hpp | 12 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/meta/operands_and_partials.hpp | 4 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/rev/scal/meta/partials_type.hpp | 11 StanHeaders-2.19.2/StanHeaders/inst/include/stan/math/version.hpp | 7 StanHeaders-2.19.2/StanHeaders/tests/rstan.R | 12 StanHeaders-2.19.2/StanHeaders/vignettes/stanmath.Rmd | 56 StanHeaders-2.21.0-1/StanHeaders/R |only StanHeaders-2.21.0-1/StanHeaders/inst/include/kinsol |only StanHeaders-2.21.0-1/StanHeaders/inst/include/src/stan/analyze/mcmc/autocovariance.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/src/stan/analyze/mcmc/compute_potential_scale_reduction.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/src/stan/analyze/mcmc/split_chains.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/src/stan/model/model_base.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/src/stan/model/model_base_crtp.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/fwd/meta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/fwd/scal/fun/beta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/fwd/scal/fun/ldexp.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/mix/mat/functor/finite_diff_grad_hessian_auto.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/mix/meta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/buffer_types.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/err/check_invalid_matrix_view.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/err/check_mat_size_one.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/err/check_opencl.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/err/check_triangular.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/err/check_vector.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/is_matrix_cl.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/bernoulli_logit_glm_lpmf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/categorical_logit_glm_lpmf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/device_functions |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/divide_columns.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/fill.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/gp_exp_quad_cov.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/neg_binomial_2_log_glm_lpmf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/normal_id_glm_lpdf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/ordered_logistic_glm_lpmf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/poisson_log_glm_lpmf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/kernels/rep_matrix.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/matrix_cl_view.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/opencl.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/prim |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/scalar_type.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/stringify.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/sub_block.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/tri_inverse.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/triangular_transpose.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/value_type.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/opencl/zeros.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/arr/fun/vec_concat.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/arr/meta/is_constant.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/core |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/core.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/eigen_plugins.h |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/err/check_flag_sundials.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/err/check_nonempty.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_gradient_auto.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_hessian_auto.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/functor/finite_diff_hessian_helper.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/meta/is_constant.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/meta/is_eigen.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/prob/bernoulli_logit_glm_rng.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/prob/categorical_logit_glm_lpmf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/prob/gaussian_dlm_obs_rng.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/prob/matrix_normal_prec_rng.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/prob/multi_normal_prec_rng.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/mat/prob/ordered_logistic_glm_lpmf.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/meta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/scal/fun/beta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/scal/fun/finite_diff_stepsize.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/scal/fun/is_any_nan.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/scal/meta/bool_constant.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/scal/meta/is_eigen.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/scal/meta/promote_args.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/prim/scal/meta/require_generics.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/core/init_chainablestack.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/mat/fun/inverse.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver_fp.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver_newton.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/mat/functor/algebra_solver_powell.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/mat/functor/kinsol_data.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/mat/functor/kinsol_solve.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/mat/functor/map_rect_concurrent.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/meta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/scal/fun/beta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/scal/fun/lbeta.hpp |only StanHeaders-2.21.0-1/StanHeaders/inst/include/stan/math/rev/scal/fun/ldexp.hpp |only StanHeaders-2.21.0-1/StanHeaders/man |only StanHeaders-2.21.0-1/StanHeaders/src/kinsol |only 1748 files changed, 43170 insertions(+), 42447 deletions(-)
Title: Statistical Disclosure Control Methods for Anonymization of Data
and Risk Estimation
Description: Data from statistical agencies and other institutions are mostly
confidential. This package (see also Templ, Kowarik and Meindl (2017) <doi:10.18637/jss.v067.i04>) can be used for the generation of anonymized
(micro)data, i.e. for the creation of public- and scientific-use files.
The theoretical basis for the methods implemented can be found in Templ (2017) <doi:10.1007/978-3-319-50272-4>.
Various risk estimation and anonymisation methods are included. Note that the package
includes a graphical user interface (Meindl and Templ, 2019 <doi:10.3390/a12090191>) that allows to use various methods of this
package.
Author: Matthias Templ [aut, cre] (<https://orcid.org/0000-0002-8638-5276>),
Bernhard Meindl [aut],
Alexander Kowarik [aut] (<https://orcid.org/0000-0001-8598-4130>)
Maintainer: Matthias Templ <matthias.templ@gmail.com>
Diff between sdcMicro versions 5.5.0 dated 2019-11-21 and 5.5.1 dated 2020-02-11
DESCRIPTION | 8 - MD5 | 36 +++---- NAMESPACE | 2 NEWS | 6 + R/microaggregation.R | 6 - R/modRisk.R | 4 R/pram.R | 156 ++++++++++++++++++--------------- R/rankSwap.R | 156 ++++++++++++++++++++++----------- R/suda2.R | 9 + build/partial.rdb |binary inst/doc/sdcMicro.R | 2 inst/doc/sdc_guidelines.R | 14 +- inst/doc/sdc_guidelines.pdf |binary inst/templates/report-template.rmd | 4 man/pram.Rd | 142 +++++++++++++++++------------- man/rankSwap.Rd | 24 +++-- man/sdcMicro-package.Rd | 2 man/sdcMicroObj-class.Rd | 2 tests/testthat/test_microaggregation.R | 2 19 files changed, 352 insertions(+), 223 deletions(-)
Title: Bayesian Applied Regression Modeling via Stan
Description: Estimates previously compiled regression models using the 'rstan'
package, which provides the R interface to the Stan C++ library for Bayesian
estimation. Users specify models via the customary R syntax with a formula and
data.frame plus some additional arguments for priors.
Author: Jonah Gabry [aut],
Imad Ali [ctb],
Sam Brilleman [ctb],
Jacqueline Buros Novik [ctb] (R/stan_jm.R),
AstraZeneca [ctb] (R/stan_jm.R),
Trustees of Columbia University [cph],
Simon Wood [cph] (R/stan_gamm4.R),
R Core Deveopment Team [cph] (R/stan_aov.R),
Douglas Bates [cph] (R/pp_data.R),
Martin Maechler [cph] (R/pp_data.R),
Ben Bolker [cph] (R/pp_data.R),
Steve Walker [cph] (R/pp_data.R),
Brian Ripley [cph] (R/stan_aov.R, R/stan_polr.R),
William Venables [cph] (R/stan_polr.R),
Paul-Christian Burkner [cph] (R/misc.R),
Ben Goodrich [cre, aut]
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstanarm versions 2.19.2 dated 2019-10-03 and 2.19.3 dated 2020-02-11
DESCRIPTION | 16 MD5 | 282 +-- NEWS.md | 51 R/bayes_R2.R | 8 R/doc-example_jm.R | 2 R/doc-example_model.R | 2 R/log_lik.R | 3 R/loo-kfold.R | 8 R/loo.R | 6 R/plots.R | 3 R/posterior_predict.R | 20 R/pp_check.R | 12 R/stan_betareg.fit.R | 2 R/stan_glm.R | 19 R/stan_glm.fit.R | 2 R/stan_lm.R | 3 R/stan_polr.fit.R | 2 build/vignette.rds |binary inst/CITATION | 18 inst/doc/aov.R | 36 inst/doc/aov.Rmd | 2 inst/doc/aov.html | 103 + inst/doc/betareg.R | 162 +- inst/doc/betareg.Rmd | 2 inst/doc/betareg.html | 200 +- inst/doc/binomial.R | 208 +- inst/doc/binomial.Rmd | 2 inst/doc/binomial.html | 236 ++- inst/doc/children/SETTINGS-knitr.txt | 2 inst/doc/continuous.R | 260 +-- inst/doc/continuous.Rmd | 2 inst/doc/continuous.html | 293 ++- inst/doc/count.R | 98 - inst/doc/count.Rmd | 2 inst/doc/count.html | 124 + inst/doc/glmer.R | 116 - inst/doc/glmer.Rmd | 2 inst/doc/glmer.html | 180 +- inst/doc/jm.R | 308 ++-- inst/doc/jm.Rmd | 2 inst/doc/jm.html | 550 ++++++- inst/doc/lm.R | 100 - inst/doc/lm.Rmd | 2 inst/doc/lm.html | 177 +- inst/doc/mrp.R | 748 ++++------ inst/doc/mrp.Rmd | 167 +- inst/doc/mrp.html | 583 ++++++- inst/doc/polr.R | 100 - inst/doc/polr.Rmd | 2 inst/doc/polr.html | 166 +- inst/doc/pooling.R | 588 +++---- inst/doc/pooling.Rmd | 4 inst/doc/pooling.html | 591 +++++-- inst/doc/priors.R | 34 inst/doc/priors.Rmd | 23 inst/doc/priors.html | 157 +- inst/doc/rstanarm.R | 206 +- inst/doc/rstanarm.Rmd | 36 inst/doc/rstanarm.html | 273 ++- inst/include/csr_matrix_times_vector2.hpp | 10 man/bayes_R2.stanreg.Rd | 8 man/example_jm.Rd | 2 man/example_model.Rd | 2 man/kfold.stanreg.Rd | 18 man/launch_shinystan.stanreg.Rd | 12 man/log_lik.stanreg.Rd | 6 man/loo.stanreg.Rd | 24 man/loo_predict.stanreg.Rd | 23 man/model.frame.stanmvreg.Rd | 3 man/pairs.stanreg.Rd | 12 man/plot.predict.stanjm.Rd | 17 man/plot.stanreg.Rd | 5 man/plot.survfit.stanjm.Rd | 13 man/posterior_interval.stanreg.Rd | 10 man/posterior_linpred.stanreg.Rd | 13 man/posterior_predict.stanreg.Rd | 47 man/posterior_survfit.Rd | 23 man/posterior_traj.Rd | 24 man/posterior_vs_prior.Rd | 13 man/pp_check.stanreg.Rd | 15 man/predict.stanreg.Rd | 9 man/predictive_error.stanreg.Rd | 11 man/predictive_interval.stanreg.Rd | 14 man/priors.Rd | 13 man/ps_check.Rd | 14 man/rstanarm-deprecated.Rd | 7 man/stan_betareg.Rd | 54 man/stan_biglm.Rd | 35 man/stan_clogit.Rd | 17 man/stan_gamm4.Rd | 40 man/stan_glm.Rd | 111 + man/stan_glmer.Rd | 72 man/stan_jm.Rd | 44 man/stan_lm.Rd | 69 man/stan_mvmer.Rd | 22 man/stan_nlmer.Rd | 21 man/stan_polr.Rd | 46 man/stanmvreg-methods.Rd | 6 man/summary.stanreg.Rd | 19 man/terms.stanmvreg.Rd | 3 src/Makevars | 6 src/stan_files/bernoulli.stan | 4 src/stan_files/continuous.stan | 7 src/stan_files/count.stan | 10 src/stan_files/data/weights_offset.stan | 2 src/stan_files/functions/SSfunctions.stan | 160 +- src/stan_files/functions/continuous_likelihoods.stan | 2 src/stan_files/functions/mvmer_functions.stan | 21 src/stan_files/model/assoc_evaluate.stan | 6 src/stan_files/model/make_eta.stan | 2 src/stan_files/polr.stan | 22 tests/testthat/helpers/expect_matrix.R | 2 tests/testthat/include/csr_matrix_times_vector2.hpp | 10 tests/testthat/stan_files/bernoulli.stan | 4 tests/testthat/stan_files/continuous.stan | 7 tests/testthat/stan_files/count.stan | 10 tests/testthat/stan_files/data/weights_offset.stan | 2 tests/testthat/stan_files/functions/SSfunctions.stan | 160 +- tests/testthat/stan_files/functions/continuous_likelihoods.stan | 2 tests/testthat/stan_files/functions/mvmer_functions.stan | 21 tests/testthat/stan_files/model/assoc_evaluate.stan | 6 tests/testthat/stan_files/model/make_eta.stan | 2 tests/testthat/stan_files/polr.stan | 22 tests/testthat/test_loo.R | 24 tests/testthat/test_methods.R | 16 tests/testthat/test_misc.R | 2 tests/testthat/test_posterior_predict.R | 7 tools/make_cc.R | 2 vignettes/aov.Rmd | 2 vignettes/betareg.Rmd | 2 vignettes/binomial.Rmd | 2 vignettes/children/SETTINGS-knitr.txt | 2 vignettes/continuous.Rmd | 2 vignettes/count.Rmd | 2 vignettes/glmer.Rmd | 2 vignettes/jm.Rmd | 2 vignettes/lm.Rmd | 2 vignettes/mrp.Rmd | 167 +- vignettes/polr.Rmd | 2 vignettes/pooling.Rmd | 4 vignettes/priors.Rmd | 23 vignettes/rstanarm.Rmd | 36 142 files changed, 5699 insertions(+), 3325 deletions(-)
Title: R Interface to Stan
Description: User-facing R functions are provided to parse, compile, test,
estimate, and analyze Stan models by accessing the header-only Stan library
provided by the 'StanHeaders' package. The Stan project develops a probabilistic
programming language that implements full Bayesian statistical inference
via Markov Chain Monte Carlo, rough Bayesian inference via 'variational'
approximation, and (optionally penalized) maximum likelihood estimation via
optimization. In all three cases, automatic differentiation is used to quickly
and accurately evaluate gradients without burdening the user with the need to
derive the partial derivatives.
Author: Jiqiang Guo [aut],
Jonah Gabry [aut],
Ben Goodrich [cre, aut],
Daniel Lee [ctb],
Krzysztof Sakrejda [ctb],
Modrak Martin [ctb],
Trustees of Columbia University [cph],
Oleg Sklyar [cph] (R/cxxfunplus.R),
The R Core Team [cph] (R/pairs.R, R/dynGet.R),
Jens Oehlschlaegel-Akiyoshi [cph] (R/pairs.R)
Maintainer: Ben Goodrich <benjamin.goodrich@columbia.edu>
Diff between rstan versions 2.19.2 dated 2019-07-09 and 2.19.3 dated 2020-02-11
DESCRIPTION | 14 MD5 | 40 +- R/cxxfunplus.R | 12 R/expose_stan_functions.R | 19 - R/extract_sparse_parts.R | 2 R/misc.R | 18 - R/monitor.R | 32 +- R/plugin.R | 4 R/rstan.R | 13 R/stanmodel-class.R | 7 R/zzz.R | 2 build/vignette.rds |binary inst/doc/SBC.R | 8 inst/doc/SBC.html | 328 ++++++++++++++++++--- inst/doc/external.R | 14 inst/doc/external.html | 441 ++++++++++++++++++++++------ inst/doc/rstan.R | 28 - inst/doc/rstan.html | 645 ++++++++++++++++++++++++++++-------------- inst/doc/stanfit-objects.R | 42 +- inst/doc/stanfit-objects.html | 563 ++++++++++++++++++++++++++---------- src/Makevars | 2 21 files changed, 1601 insertions(+), 633 deletions(-)
Title: Bayesian Logistic Regression for Oncology Dose-Escalation Trials
Description: Bayesian logistic regression model with optional
EXchangeability-NonEXchangeability parameter modelling for flexible
borrowing from historical or concurrent data-sources. The safety model
can guide dose-escalation decisions for adaptive oncology Phase I
dose-escalation trials which involve an arbitrary number of
drugs. Please refer to Neuenschwander et al. (2008)
<doi:10.1002/sim.3230> and Neuenschwander et al. (2016)
<doi:10.1080/19466315.2016.1174149> for details on the methodology.
Author: Novartis Pharma AG [cph],
Sebastian Weber [aut, cre],
Andrew Bean [aut],
Lukas A. Widmer [aut],
Trustees of Columbia University [cph] (R/stanmodels.R, configure,
configure.win)
Maintainer: Sebastian Weber <sebastian.weber@novartis.com>
Diff between OncoBayes2 versions 0.5-8 dated 2019-12-12 and 0.6-0 dated 2020-02-11
OncoBayes2-0.5-8/OncoBayes2/inst/sbc/launch_sbc.sh |only OncoBayes2-0.6-0/OncoBayes2/DESCRIPTION | 10 OncoBayes2-0.6-0/OncoBayes2/MD5 | 41 OncoBayes2-0.6-0/OncoBayes2/R/blrm_exnex.R | 8 OncoBayes2-0.6-0/OncoBayes2/R/sysdata.rda |binary OncoBayes2-0.6-0/OncoBayes2/inst/NEWS | 8 OncoBayes2-0.6-0/OncoBayes2/inst/doc/OncoBayes2.pdf |binary OncoBayes2-0.6-0/OncoBayes2/inst/doc/introduction.R | 2 OncoBayes2-0.6-0/OncoBayes2/inst/doc/introduction.Rmd | 2 OncoBayes2-0.6-0/OncoBayes2/inst/doc/introduction.html | 292 +-- OncoBayes2-0.6-0/OncoBayes2/inst/sbc/calibration.md5 | 6 OncoBayes2-0.6-0/OncoBayes2/inst/sbc/make_reference_rankhist.R | 38 OncoBayes2-0.6-0/OncoBayes2/inst/sbc/sbc_example_models.R | 190 +- OncoBayes2-0.6-0/OncoBayes2/inst/sbc/sbc_report.R | 49 OncoBayes2-0.6-0/OncoBayes2/inst/sbc/sbc_report.html | 740 +++++++--- OncoBayes2-0.6-0/OncoBayes2/inst/sbc/sbc_tools.R | 249 +-- OncoBayes2-0.6-0/OncoBayes2/inst/stan/blrm_exnex.stan | 6 OncoBayes2-0.6-0/OncoBayes2/src/stanExports_blrm_exnex.h | 11 OncoBayes2-0.6-0/OncoBayes2/tests/testthat/helper-trial_examples.R | 22 OncoBayes2-0.6-0/OncoBayes2/tests/testthat/test-blrm_trial.R | 48 OncoBayes2-0.6-0/OncoBayes2/tools/build.sh | 2 OncoBayes2-0.6-0/OncoBayes2/vignettes/introduction.Rmd | 2 22 files changed, 1147 insertions(+), 579 deletions(-)
Title: Datasets for Spatial Analysis
Description: Diverse spatial datasets for demonstrating, benchmarking and teaching spatial data analysis.
It includes R data of class sf (defined by the package 'sf'), Spatial ('sp'), and nb ('spdep').
Unlike other spatial data packages such as 'rnaturalearth' and 'maps',
it also contains data stored in a range of file formats including GeoJSON, ESRI Shapefile and GeoPackage.
Some of the datasets are designed to illustrate specific analysis techniques.
cycle_hire() and cycle_hire_osm(), for example, is designed to illustrate point pattern analysis techniques.
Author: Roger Bivand [aut] (<https://orcid.org/0000-0003-2392-6140>),
Jakub Nowosad [aut, cre] (<https://orcid.org/0000-0002-1057-3721>),
Robin Lovelace [aut] (<https://orcid.org/0000-0001-5679-6536>),
Mark Monmonier [ctb] (author of the state.vbm dataset),
Greg Snow [ctb] (author of the state.vbm dataset)
Maintainer: Jakub Nowosad <nowosad.jakub@gmail.com>
Diff between spData versions 0.3.2 dated 2019-09-19 and 0.3.3 dated 2020-02-11
DESCRIPTION | 13 +++++++------ MD5 | 24 ++++++++++++------------ NAMESPACE | 3 +++ R/SplashDams.R | 1 + R/elect80.R | 1 + R/elev.R | 3 ++- R/grain.R | 3 ++- R/house.R | 1 + R/state.vbm.R | 1 + R/urban_agglomerations.R | 2 +- man/elev.Rd | 2 +- man/grain.Rd | 2 +- man/urban_agglomerations.Rd | 2 +- 13 files changed, 34 insertions(+), 24 deletions(-)
Title: Penalized Multi-Band Learning for Circadian Rhythm Analysis
Using Actigraphy
Description: Penalized Multi-Band Learning algorithm can be effectively implemented for circadian rhythm analysis and daily activity pattern characterization using actigraphy (continuously measured objective physical activity data). Functions for interactive visualization of actigraph data are also included. Method reference: Li, X., Kane, M., Zhang, Y., Sun, W., Song, Y., Dong, S., Lin, Q., Zhu, Q., Jiang, F., Zhao, H. (2019) A Novel Penalized Multi-band Learning Approach Characterizes the Consolidation of Sleep-Wake Circadian Rhythms During Early Childhood Development.
Author: Xinyue Li [aut, cre],
Michael Kane [aut]
Maintainer: Xinyue Li <xinyue.li@yale.edu>
Diff between PML versions 1.1 dated 2019-09-17 and 1.2 dated 2020-02-11
DESCRIPTION | 10 +++--- MD5 | 10 +++--- NAMESPACE | 2 - R/tre.R | 78 +++++++++++++++++++++++++++++------------------------- build/partial.rdb |binary inst/doc/PML.html | 5 +-- 6 files changed, 54 insertions(+), 51 deletions(-)
Title: Methods for Graphical Models and Causal Inference
Description: Functions for causal structure
learning and causal inference using graphical models. The main algorithms
for causal structure learning are PC (for observational data without hidden
variables), FCI and RFCI (for observational data with hidden variables),
and GIES (for a mix of data from observational studies
(i.e. observational data) and data from experiments
involving interventions (i.e. interventional data) without hidden
variables). For causal inference the IDA algorithm, the Generalized
Backdoor Criterion (GBC), the Generalized Adjustment Criterion (GAC)
and some related functions are implemented. Functions for incorporating
background knowledge are provided.
Author: Markus Kalisch [aut, cre],
Alain Hauser [aut],
Martin Maechler [aut],
Diego Colombo [ctb],
Doris Entner [ctb],
Patrik Hoyer [ctb],
Antti Hyttinen [ctb],
Jonas Peters [ctb],
Nicoletta Andri [ctb],
Emilija Perkovic [ctb],
Preetam Nandy [ctb],
Philipp Ruetimann [ctb],
Daniel Stekhoven [ctb],
Manuel Schuerch [ctb],
Marco Eigenmann [ctb]
Maintainer: Markus Kalisch <kalisch@stat.math.ethz.ch>
Diff between pcalg versions 2.6-8 dated 2019-11-21 and 2.6-9 dated 2020-02-11
DESCRIPTION | 8 ++++---- MD5 | 16 ++++++++-------- R/pcalg.R | 2 +- build/vignette.rds |binary inst/doc/pcalgDoc.pdf |binary inst/doc/vignette2018.pdf |binary man/dag2essgraph.Rd | 7 ++----- src/gies.cpp | 4 ++-- tests/test_rmvDAG.R | 11 +++++++++++ 9 files changed, 28 insertions(+), 20 deletions(-)
Title: Linguistic Fuzzy Logic
Description: Various algorithms related to linguistic fuzzy logic: mining for linguistic fuzzy association
rules, composition of fuzzy relations, performing perception-based logical deduction (PbLD),
and forecasting time-series using fuzzy rule-based ensemble (FRBE).
Author: Michal Burda
Maintainer: Michal Burda <michal.burda@osu.cz>
Diff between lfl versions 1.4.2 dated 2018-08-01 and 2.0 dated 2020-02-11
lfl-1.4.2/lfl/R/as.data.frame.farules.R |only lfl-1.4.2/lfl/R/as.matrix.fsets.R |only lfl-1.4.2/lfl/R/cbind.fsets.R |only lfl-1.4.2/lfl/R/fcut.data.frame.R |only lfl-1.4.2/lfl/R/fcut.default.R |only lfl-1.4.2/lfl/R/fcut.matrix.R |only lfl-1.4.2/lfl/R/fcut.numeric.R |only lfl-1.4.2/lfl/R/fset.R |only lfl-1.4.2/lfl/R/head.farules.R |only lfl-1.4.2/lfl/R/head.fsets.R |only lfl-1.4.2/lfl/R/is.algebra.R |only lfl-1.4.2/lfl/R/is.farules.R |only lfl-1.4.2/lfl/R/is.fsets.R |only lfl-1.4.2/lfl/R/lcut.data.frame.R |only lfl-1.4.2/lfl/R/lcut.default.R |only lfl-1.4.2/lfl/R/lcut.matrix.R |only lfl-1.4.2/lfl/R/lcut.numeric.R |only lfl-1.4.2/lfl/R/plot.fsets.R |only lfl-1.4.2/lfl/R/print.farules.R |only lfl-1.4.2/lfl/R/print.fsets.R |only lfl-1.4.2/lfl/R/raisedcos.R |only lfl-1.4.2/lfl/R/sel.R |only lfl-1.4.2/lfl/R/sel.farules.R |only lfl-1.4.2/lfl/R/sel.fsets.R |only lfl-1.4.2/lfl/R/slices.R |only lfl-1.4.2/lfl/R/specs.R |only lfl-1.4.2/lfl/R/tail.farules.R |only lfl-1.4.2/lfl/R/tail.fsets.R |only lfl-1.4.2/lfl/R/triangle.R |only lfl-1.4.2/lfl/R/vars.R |only lfl-1.4.2/lfl/man/as.matrix.fsets.Rd |only lfl-1.4.2/lfl/man/errors.Rd |only lfl-1.4.2/lfl/man/head.farules.Rd |only lfl-1.4.2/lfl/man/head.fsets.Rd |only lfl-1.4.2/lfl/man/sel.Rd |only lfl-1.4.2/lfl/man/tail.farules.Rd |only lfl-1.4.2/lfl/man/tail.fsets.Rd |only lfl-1.4.2/lfl/src/algebra.h |only lfl-1.4.2/lfl/src/isSpecific.cpp |only lfl-1.4.2/lfl/src/isSpecific.h |only lfl-1.4.2/lfl/src/lfl_init.c |only lfl-1.4.2/lfl/src/mult.h |only lfl-1.4.2/lfl/src/pbld |only lfl-1.4.2/lfl/src/perceiveGlobal.cpp |only lfl-1.4.2/lfl/src/perceiveGlobal.h |only lfl-1.4.2/lfl/src/reduce.h |only lfl-1.4.2/lfl/src/search.h |only lfl-1.4.2/lfl/tests/testthat/test-fcut.factor.R |only lfl-1.4.2/lfl/tests/testthat/test-fcut.numeric.R |only lfl-1.4.2/lfl/tests/testthat/test-is.algebra.R |only lfl-1.4.2/lfl/tests/testthat/test-lcut.data.frame.R |only lfl-1.4.2/lfl/tests/testthat/test-lcut.matrix.R |only lfl-1.4.2/lfl/tests/testthat/test-lcut.numeric.R |only lfl-1.4.2/lfl/tests/testthat/test-raisedcos.R |only lfl-1.4.2/lfl/tests/testthat/test-sel.farules.R |only lfl-1.4.2/lfl/tests/testthat/test-sel.fsets.R |only lfl-1.4.2/lfl/tests/testthat/test-slices.R |only lfl-1.4.2/lfl/tests/testthat/test-triangle.R |only lfl-2.0/lfl/DESCRIPTION | 17 lfl-2.0/lfl/MD5 | 269 ++-- lfl-2.0/lfl/NAMESPACE | 216 ++- lfl-2.0/lfl/R/RcppExports.R |only lfl-2.0/lfl/R/aggregateConsequents.R | 125 +- lfl-2.0/lfl/R/algebra.R | 307 ++++- lfl-2.0/lfl/R/algebraNA.R |only lfl-2.0/lfl/R/antecedents.R | 27 lfl-2.0/lfl/R/compose.R | 116 +- lfl-2.0/lfl/R/consequents.R | 28 lfl-2.0/lfl/R/ctx.R |only lfl-2.0/lfl/R/defuzz.R | 66 - lfl-2.0/lfl/R/evalfrbe.R | 53 lfl-2.0/lfl/R/exprs.R |only lfl-2.0/lfl/R/exprsDeprecated.R |only lfl-2.0/lfl/R/farules.R | 136 ++ lfl-2.0/lfl/R/fcut.R | 386 +++++++ lfl-2.0/lfl/R/fire.R | 128 ++ lfl-2.0/lfl/R/frbe.R | 112 +- lfl-2.0/lfl/R/frbemodel.R | 926 ++++++++--------- lfl-2.0/lfl/R/fsets.R | 391 ++++++- lfl-2.0/lfl/R/hedge.R |only lfl-2.0/lfl/R/horizon.R |only lfl-2.0/lfl/R/is.frbe.R | 20 lfl-2.0/lfl/R/is.specific.R | 139 +- lfl-2.0/lfl/R/lcut.R | 287 +++++ lfl-2.0/lfl/R/lcutDeprecated.R |only lfl-2.0/lfl/R/lfl-package.R |only lfl-2.0/lfl/R/lingexpr.R |only lfl-2.0/lfl/R/mase.R | 21 lfl-2.0/lfl/R/minmax.R |only lfl-2.0/lfl/R/mult.R | 53 lfl-2.0/lfl/R/pbld.R | 117 +- lfl-2.0/lfl/R/perceive.R | 129 +- lfl-2.0/lfl/R/print.frbe.R | 33 lfl-2.0/lfl/R/rbcoverage.R | 74 + lfl-2.0/lfl/R/reduce.R | 75 + lfl-2.0/lfl/R/rmse.R | 22 lfl-2.0/lfl/R/searchrules.R | 174 +-- lfl-2.0/lfl/R/slicesDeprecated.R |only lfl-2.0/lfl/R/smape.R | 25 lfl-2.0/lfl/R/testers.R |only lfl-2.0/lfl/README.md |only lfl-2.0/lfl/configure | 16 lfl-2.0/lfl/configure.ac | 2 lfl-2.0/lfl/man/aggregateConsequents.Rd | 144 +- lfl-2.0/lfl/man/algebra.Rd | 345 ++---- lfl-2.0/lfl/man/antecedents.Rd | 56 - lfl-2.0/lfl/man/as.data.frame.farules.Rd | 61 - lfl-2.0/lfl/man/as.data.frame.fsets.Rd |only lfl-2.0/lfl/man/c.farules.Rd |only lfl-2.0/lfl/man/cbind.fsets.Rd | 78 - lfl-2.0/lfl/man/compose.Rd | 126 +- lfl-2.0/lfl/man/consequents.Rd | 57 - lfl-2.0/lfl/man/ctx.Rd |only lfl-2.0/lfl/man/defaultHedgeParams.Rd |only lfl-2.0/lfl/man/defuzz.Rd | 112 -- lfl-2.0/lfl/man/evalfrbe.Rd | 94 - lfl-2.0/lfl/man/farules.Rd | 63 - lfl-2.0/lfl/man/fcut.Rd | 323 +++-- lfl-2.0/lfl/man/fire.Rd | 157 +- lfl-2.0/lfl/man/frbe.Rd | 140 +- lfl-2.0/lfl/man/fsets.Rd | 144 +- lfl-2.0/lfl/man/hedge.Rd |only lfl-2.0/lfl/man/horizon.Rd |only lfl-2.0/lfl/man/is.farules.Rd | 41 lfl-2.0/lfl/man/is.frbe.Rd | 52 lfl-2.0/lfl/man/is.fsets.Rd | 43 lfl-2.0/lfl/man/is.specific.Rd | 137 +- lfl-2.0/lfl/man/lcut.Rd | 393 ++----- lfl-2.0/lfl/man/lcut3.Rd |only lfl-2.0/lfl/man/lfl.Rd |only lfl-2.0/lfl/man/lingexpr.Rd |only lfl-2.0/lfl/man/mase.Rd |only lfl-2.0/lfl/man/minmax.Rd |only lfl-2.0/lfl/man/mult.Rd | 81 - lfl-2.0/lfl/man/pbld.Rd | 167 +-- lfl-2.0/lfl/man/perceive.Rd | 172 +-- lfl-2.0/lfl/man/plot.fsets.Rd | 74 - lfl-2.0/lfl/man/print.farules.Rd | 56 - lfl-2.0/lfl/man/print.frbe.Rd | 65 - lfl-2.0/lfl/man/print.fsets.Rd | 57 - lfl-2.0/lfl/man/rbcoverage.Rd | 120 +- lfl-2.0/lfl/man/reduce.Rd | 136 +- lfl-2.0/lfl/man/rmse.Rd |only lfl-2.0/lfl/man/searchrules.Rd | 233 ++-- lfl-2.0/lfl/man/slices.Rd | 73 - lfl-2.0/lfl/man/smape.Rd |only lfl-2.0/lfl/man/sobocinski.Rd |only lfl-2.0/lfl/man/triangle.Rd | 77 - lfl-2.0/lfl/man/triangular.Rd |only lfl-2.0/lfl/src/RcppExports.cpp |only lfl-2.0/lfl/src/algebra.cpp | 198 +-- lfl-2.0/lfl/src/common.h | 14 lfl-2.0/lfl/src/exprs.cpp |only lfl-2.0/lfl/src/hedge.cpp |only lfl-2.0/lfl/src/mult.cpp | 12 lfl-2.0/lfl/src/reduce.cpp | 8 lfl-2.0/lfl/src/search.cpp | 9 lfl-2.0/lfl/src/search/Search.h | 3 lfl-2.0/lfl/src/search/Task.h | 23 lfl-2.0/lfl/src/specificity.cpp |only lfl-2.0/lfl/tests/testthat/test-aggregateConsequents.R | 10 lfl-2.0/lfl/tests/testthat/test-algebra.R | 326 +++-- lfl-2.0/lfl/tests/testthat/test-algebraNA.R |only lfl-2.0/lfl/tests/testthat/test-antecedents.R | 14 lfl-2.0/lfl/tests/testthat/test-cbind.fsets.R | 43 lfl-2.0/lfl/tests/testthat/test-composeNA.R |only lfl-2.0/lfl/tests/testthat/test-consequents.R | 21 lfl-2.0/lfl/tests/testthat/test-ctx.R |only lfl-2.0/lfl/tests/testthat/test-defuzz.R | 9 lfl-2.0/lfl/tests/testthat/test-exprs.R |only lfl-2.0/lfl/tests/testthat/test-farules.R |only lfl-2.0/lfl/tests/testthat/test-fcut.R |only lfl-2.0/lfl/tests/testthat/test-fire.R | 66 - lfl-2.0/lfl/tests/testthat/test-fsets.R |only lfl-2.0/lfl/tests/testthat/test-hedge.R |only lfl-2.0/lfl/tests/testthat/test-horizon.R |only lfl-2.0/lfl/tests/testthat/test-is.specific.R | 142 +- lfl-2.0/lfl/tests/testthat/test-lcut.R |only lfl-2.0/lfl/tests/testthat/test-lcutDeprecated.R |only lfl-2.0/lfl/tests/testthat/test-lingexpr.R |only lfl-2.0/lfl/tests/testthat/test-mase.R | 3 lfl-2.0/lfl/tests/testthat/test-minmax.R |only lfl-2.0/lfl/tests/testthat/test-pbld.R | 40 lfl-2.0/lfl/tests/testthat/test-perceive.R | 94 - lfl-2.0/lfl/tests/testthat/test-rmse.R | 3 lfl-2.0/lfl/tests/testthat/test-searchrules.R | 36 lfl-2.0/lfl/tests/testthat/test-smape.R | 3 lfl-2.0/lfl/tests/testthat/test-testers.R |only 188 files changed, 5669 insertions(+), 3775 deletions(-)
Title: Less Code, More Results
Description: Each function accomplishes the work of several or more standard R functions. For example, two function calls, Read() and CountAll(), read the data and generate summary statistics for all variables in the data frame, plus histograms and bar charts as appropriate. Other functions provide for descriptive statistics, a comprehensive regression analysis, analysis of variance and t-test, plotting including the introduced here Violin/Box/Scatter plot for a numerical variable, bar chart, histogram, box plot, density curves, calibrated power curve, reading multiple data formats with the same function call, variable labels, color themes, Trellis graphics and a built-in help system. Also includes a confirmatory factor analysis of multiple indicator measurement models, pedagogical routines for data simulation such as for the Central Limit Theorem, and generation and rendering of R markdown instructions for interpretative output.
Author: David Gerbing, The School of Business, Portland State University
Maintainer: David W. Gerbing <gerbing@pdx.edu>
Diff between lessR versions 3.9.0 dated 2019-12-07 and 3.9.2 dated 2020-02-11
DESCRIPTION | 14 +-- MD5 | 59 +++++++------- NEWS | 57 ++++++++++++++ R/Help.R | 4 - R/Plot.R | 12 +-- R/Regression.R | 195 +++++++++++++++++++++++++++---------------------- R/corCFA.R | 25 ++---- R/corEFA.R | 32 +++++--- R/corRead.R | 21 +++-- R/details.R | 4 - R/logit.z4Pred.R | 206 +++++++++++++++++++++++++--------------------------- R/logit.z5Confuse.R |only R/plt.zlattice.R | 68 ++++++++++------- R/plt.zmain.R | 6 - R/plt.zpanel.R | 2 R/plt.ztxt.R | 2 R/simCImean.R | 21 +++-- R/simCLT.R | 17 ++-- R/simFlips.R | 20 +++-- R/simMeans.R | 60 +++++++++------ R/zzz.R | 10 +- man/Logit.Rd | 53 +++++++------ man/Plot.Rd | 7 + man/Regression.Rd | 3 man/corCFA.Rd | 13 ++- man/corRead.Rd | 20 ++--- man/corScree.Rd | 2 man/simCImean.Rd | 37 ++++++--- man/simCLT.Rd | 34 ++++++-- man/simFlips.Rd | 24 ++++-- man/simMeans.Rd | 24 ++++-- 31 files changed, 618 insertions(+), 434 deletions(-)
Title: File Handlers for Genomic Data Analysis
Description: A collection of I/O tools for handling the most commonly used genomic datafiles, like fasta/-q, bed, gff, gtf, ped/map and vcf.
Author: Daniel Fischer
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between GenomicTools.fileHandler versions 0.1.4 dated 2019-02-06 and 0.1.5.8 dated 2020-02-11
DESCRIPTION | 8 MD5 | 35 ++-- NAMESPACE | 6 R/GenomicTools.fileHandler.R | 2 R/S3print.R | 22 ++ R/S3summary.STARLog.R |only R/aaa.R | 2 R/importFA.R | 30 ++- R/importFQ.R | 4 R/importSTARLog.R | 206 ++++++++++++++++++++++++- R/importVCF.R | 18 +- R/plotTotalReads.R |only R/plotUniquelyMappedReads.R |only inst/ChangeLog | 11 + inst/doc/GenomicTools.fileHandler-Vignette.pdf |binary man/GenomicTools.fileHandler-package.Rd | 2 man/importFA.Rd | 5 man/importSTARLog.Rd | 13 + man/plotTotalReads.Rd |only man/plotUniquelyMappedReads.Rd |only man/print.gtf.Rd |only man/summary.STARLog.Rd |only 22 files changed, 315 insertions(+), 49 deletions(-)
More information about GenomicTools.fileHandler at CRAN
Permanent link
Title: Spatial ARCH and GARCH Models (spGARCH)
Description: A collection of functions to deal with spatial and spatiotemporal autoregressive conditional heteroscedasticity (spatial ARCH and GARCH models) by Otto, Schmid, Garthoff (2018, Spatial Statistics) <arXiv:1609.00711>: simulation of spatial ARCH-type processes (spARCH, exponential spARCH, complex spARCH); quasi-maximum-likelihood estimation of the parameters of spARCH models and spatial autoregressive models with spARCH disturbances, diagnostic checks, visualizations.
Author: Philipp Otto [cre, aut] (<https://orcid.org/0000-0002-9796-6682>)
Maintainer: Philipp Otto <potto@europa-uni.de>
Diff between spGARCH versions 0.2.0 dated 2019-08-25 and 0.2.1 dated 2020-02-11
DESCRIPTION | 6 - MD5 | 12 +- R/Estimation.R | 230 ++++++++++++++++++++++++++++++++++++++++++++++--- R/Simulations.R | 10 +- man/prostate_cancer.Rd | 6 - man/qml.SARspARCH.Rd | 6 - man/qml.spARCH.Rd | 6 - 7 files changed, 244 insertions(+), 32 deletions(-)
Title: Multiple Pairwise Comparison Tests
Description: Multiple pairwise comparison tests on tidy data for
one-way analysis of variance for both between-subjects and
within-subjects designs. Currently, it supports only the most common
types of statistical analyses and tests: parametric (Welch's and
Student's t-test), nonparametric (Durbin-Conover test and
Dwass-Steel-Crichtlow-Fligner test), robust (Yuen’s trimmed means
test).
Author: Indrajeet Patil [cre, aut, ctb]
(<https://orcid.org/0000-0003-1995-6531>)
Maintainer: Indrajeet Patil <patilindrajeet.science@gmail.com>
Diff between pairwiseComparisons versions 0.2.0 dated 2020-02-02 and 0.2.5 dated 2020-02-11
pairwiseComparisons-0.2.0/pairwiseComparisons/R/utils_formatting.R |only pairwiseComparisons-0.2.0/pairwiseComparisons/man/long_to_wide_converter.Rd |only pairwiseComparisons-0.2.0/pairwiseComparisons/man/signif_column.Rd |only pairwiseComparisons-0.2.0/pairwiseComparisons/man/specify_decimal_p.Rd |only pairwiseComparisons-0.2.0/pairwiseComparisons/tests/testthat/test-long_to_wide_converter.R |only pairwiseComparisons-0.2.5/pairwiseComparisons/DESCRIPTION | 14 pairwiseComparisons-0.2.5/pairwiseComparisons/MD5 | 29 - pairwiseComparisons-0.2.5/pairwiseComparisons/NAMESPACE | 22 pairwiseComparisons-0.2.5/pairwiseComparisons/NEWS.md | 6 pairwiseComparisons-0.2.5/pairwiseComparisons/R/pairwise_comparisons.R | 32 - pairwiseComparisons-0.2.5/pairwiseComparisons/R/reexports.R | 31 + pairwiseComparisons-0.2.5/pairwiseComparisons/README.md | 246 ++++++---- pairwiseComparisons-0.2.5/pairwiseComparisons/inst/WORDLIST | 1 pairwiseComparisons-0.2.5/pairwiseComparisons/inst/doc/tests_and_coverage.Rmd | 25 - pairwiseComparisons-0.2.5/pairwiseComparisons/inst/doc/tests_and_coverage.html | 49 - pairwiseComparisons-0.2.5/pairwiseComparisons/man/reexports.Rd | 6 pairwiseComparisons-0.2.5/pairwiseComparisons/tests/README.md | 27 - pairwiseComparisons-0.2.5/pairwiseComparisons/vignettes/tests_and_coverage.Rmd | 25 - 18 files changed, 288 insertions(+), 225 deletions(-)
More information about pairwiseComparisons at CRAN
Permanent link
Title: Automatic Shift Detection using a Phylogenetic EM
Description: Implementation of the automatic shift detection method for
Brownian Motion (BM) or Ornstein–Uhlenbeck (OU) models of trait evolution on
phylogenies. Some tools to handle equivalent shifts configurations are also
available. See Bastide et al. (2017) <doi:10.1111/rssb.12206> and
Bastide et al. (2018) <doi:10.1093/sysbio/syy005>.
Author: Paul Bastide [aut, cre],
Mahendra Mariadassou [ctb]
Maintainer: Paul Bastide <paul.bastide@m4x.org>
Diff between PhylogeneticEM versions 1.3.0 dated 2019-10-03 and 1.4.0 dated 2020-02-11
DESCRIPTION | 8 MD5 | 257 ++++++++++---------- NEWS.md | 14 - R/E_step.R | 137 ++++++++-- R/M_step.R | 94 +++---- R/estimateEM.R | 20 - R/generic_functions.R | 26 +- R/init_EM.R | 2 R/model_selection.R | 2 R/parsimonyNumber.R | 101 +++---- R/partitionsNumber.R | 44 +-- R/plot_functions.R | 20 + R/shifts_manipulations.R | 62 ++-- R/simulate.R | 91 +++++-- build/vignette.rds |binary inst/CITATION | 4 inst/WORDLIST |only inst/doc/monkeys.R | 36 +- inst/doc/monkeys.Rmd | 2 inst/doc/monkeys.html | 28 +- inst/doc/tutorial.R | 40 +-- inst/doc/tutorial.Rmd | 10 inst/doc/tutorial.html | 75 ++--- man/PhyloEM.Rd | 54 ++-- man/allocate_regimes_from_shifts.Rd | 2 man/allocate_shifts_from_regimes.Rd | 2 man/allocate_subset_node.simulate.Rd | 2 man/check.selection.strength.Rd | 3 man/check_dimensions.Rd | 10 man/check_range_alpha.Rd | 2 man/clusters_from_shifts.Rd | 3 man/compute_E.simple.Rd | 29 +- man/compute_actualization_matrix_ultrametric.Rd | 11 man/compute_betas_from_shifts.Rd | 2 man/compute_diff_exp.BM.Rd | 2 man/compute_dist_phy.Rd | 2 man/compute_expectations.BM.Rd | 2 man/compute_expectations.scOU.Rd | 12 man/compute_gauss_lasso.Rd | 9 man/compute_log_likelihood.simple.Rd | 15 - man/compute_mahalanobis_distance.simple.Rd | 11 man/compute_mean_variance.simple.Rd | 17 - man/compute_shifts_from_betas.Rd | 2 man/compute_times_ca.Rd | 4 man/compute_tree_correlations_matrix.scOU.Rd | 8 man/compute_var_diff.BM.Rd | 2 man/compute_variance_block_diagonal.BM.Rd |only man/compute_variance_block_diagonal.OU.Rd |only man/compute_variance_covariance.OU.Rd | 3 man/compute_variance_covariance.OU.nonsym.Rd | 8 man/compute_variance_covariance.scOU.Rd | 8 man/enumerate_parsimony.Rd | 2 man/enumerate_tips_under_edges.Rd | 2 man/equivalent_shifts.Rd | 77 +++-- man/equivalent_shifts_edges.Rd | 7 man/equivalent_shifts_values.Rd | 2 man/estimate.alpha.Rd | 11 man/estimateEM.Rd | 68 +++-- man/extract.enumerate_parsimony.Rd | 10 man/extract.equivalent_shifts.Rd | 3 man/extract.parsimonyNumber.Rd | 8 man/extract.partitionsNumber.Rd | 9 man/extract.simul_process.Rd | 8 man/extract.variance_covariance.Rd | 16 - man/find_grid_alpha.Rd | 15 - man/find_rotation.Rd | 4 man/get_variance_node.Rd | 2 man/go_back_to_original_process.Rd | 8 man/imputed_traits.Rd | 15 - man/incidence.matrix.Rd | 2 man/incidence.matrix.full.Rd | 2 man/incidence_matrix_actualization_factors.Rd | 16 - man/init.EM.lasso.Rd | 41 ++- man/init.allocate_regimes_from_shifts.Rd | 2 man/init.alpha.gamma.estimation.Rd | 26 +- man/init.compute_betas_from_shifts.Rd | 2 man/init.enumerate_parsimony.Rd | 6 man/init.incidence.matrix.Rd | 4 man/init.incidence.matrix.full.Rd | 4 man/init.parsimonyCost.Rd | 4 man/init.parsimonyNumber.Rd | 4 man/init.simulate.BM.Rd | 2 man/init.simulate.OU.Rd | 2 man/init.simulate.StateAndExp.Rd | 2 man/lasso_regression_K_fixed.glmnet_multivariate.Rd | 12 man/merge_rotations.Rd | 4 man/model_selection.Rd | 12 man/params_BM.Rd | 20 + man/params_OU.Rd | 23 + man/params_process.PhyloEM.Rd | 11 man/parsimonyCost.Rd | 2 man/parsimonyNumber.Rd | 2 man/partitionsNumber.Rd | 42 +-- man/penalty_BirgeMassart_shape1.Rd | 2 man/penalty_pBIC.Rd | 15 + man/plot.PhyloEM.Rd | 50 ++- man/plot.enumerate_parsimony.Rd | 3 man/plot.equivalent_shifts.Rd | 16 - man/plot.params_process.Rd | 43 ++- man/plot_criterion.Rd | 11 man/sample_shifts_edges.Rd | 3 man/scale_params.Rd | 2 man/segmentation.OU.specialCase.lasso.Rd | 10 man/shifts.list_to_matrix.Rd | 2 man/shifts_to_simmap.Rd | 2 man/simul_process.Rd | 27 +- man/simulate_internal.Rd | 28 +- man/test.root.state.Rd | 2 man/update.compute_betas_from_shifts.Rd | 2 man/update.enumerate_parsimony.Rd | 11 man/update.incidence.matrix.full.Rd | 2 man/update.parsimonyNumber.Rd | 2 man/wrapper_E_step.Rd | 18 + tests/testthat/test-EM-no_missing.R | 1 tests/testthat/test-core-log_likelihood.R | 2 tests/testthat/test-independent_multivariate.R | 3 tests/testthat/test-shifts-model_selection.R | 1 tests/testthat/test-shifts-parsimonyNumber.R | 2 tests/testthat/test-shifts-partitionsNumber.R | 2 tests/testthat/test-upward_downward.R | 10 tests/testthat/test-utilities-handling_parameters.R | 1 tests/testthat/test-utilities-impute-traits.R | 2 tests/testthat/test-utilities-simulate.R | 90 +++++++ tests/testthat_EM.R | 12 tests/testthat_core.R | 12 tests/testthat_independent.R | 12 tests/testthat_shifts.R | 11 tests/testthat_upward.R | 12 tests/testthat_utilities.R | 12 vignettes/monkeys.Rmd | 2 vignettes/tutorial.Rmd | 10 131 files changed, 1450 insertions(+), 810 deletions(-)
More information about PhylogeneticEM at CRAN
Permanent link
Title: Computing P-Values of the K-S Test for (Dis)Continuous Null
Distribution
Description: Computes a p-value of the one-sample two-sided (or one-sided, as a special case) Kolmogorov-Smirnov (KS) statistic, for any fixed critical level, and an arbitrary, possibly large sample size for a pre-specified purely discrete, mixed or continuous cumulative distribution function (cdf) under the null hypothesis. If a data sample is supplied, 'KSgeneral' computes the p-value corresponding to the value of the KS test statistic computed based on the user provided data sample. The package 'KSgeneral' implements a novel, accurate and efficient method named Exact-KS-FFT, expressing the p-value as a double-boundary non-crossing probability for a homogeneous Poisson process, which is then efficiently computed using Fast Fourier Transform (FFT). The package can also be used to compute and plot the complementary cdf of the KS statistic which is known to depend on the hypothesized distribution when the latter is discontinuous (i.e. purely discrete or mixed).
Author: Dimitrina S. Dimitrova <D.Dimitrova@city.ac.uk>,
Vladimir K. Kaishev <Vladimir.Kaishev.1@city.ac.uk> and
Senren Tan <senren.tan@cass.city.ac.uk>
Maintainer: Senren Tan <senren.tan@cass.city.ac.uk>
Diff between KSgeneral versions 0.1.1 dated 2018-05-14 and 0.1.2 dated 2020-02-11
DESCRIPTION | 6 MD5 | 8 build/partial.rdb |binary configure | 720 ------------------------------------------------------ configure.ac | 5 5 files changed, 13 insertions(+), 726 deletions(-)
Title: Geographically Weighted Regression
Description: Functions for computing geographically weighted
regressions are provided, based on work by Chris
Brunsdon, Martin Charlton and Stewart Fotheringham.
Author: Roger Bivand [cre, aut] (<https://orcid.org/0000-0003-2392-6140>),
Danlin Yu [aut],
Tomoki Nakaya [ctb],
Miquel-Angel Garcia-Lopez [ctb]
Maintainer: Roger Bivand <Roger.Bivand@nhh.no>
Diff between spgwr versions 0.6-32 dated 2017-10-29 and 0.6-33 dated 2020-02-11
ChangeLog | 350 +++-------------------------------------------------- DESCRIPTION | 11 - MD5 | 12 - R/gwr.R | 4 build/vignette.rds |binary inst/doc/GWR.pdf |binary man/georgia.Rd | 2 7 files changed, 35 insertions(+), 344 deletions(-)
Title: Distance to Default
Description: Provides fast methods to work with Merton's distance to default
model introduced in Merton (1974) <doi:10.1111/j.1540-6261.1974.tb03058.x>.
The methods includes simulation and estimation of the parameters.
Author: Benjamin Christoffersen [cre, aut],
R-core [cph],
Robert Gentleman [cph],
Ross Ihaka [cph]
Maintainer: Benjamin Christoffersen <boennecd@gmail.com>
Diff between DtD versions 0.2.1 dated 2019-01-10 and 0.2.2 dated 2020-02-11
DESCRIPTION | 18 - MD5 | 68 ++-- NAMESPACE | 38 +- NEWS.md | 21 - R/BS_call.R | 32 +- R/BS_fit.R | 218 +++++++------- R/BS_sim.R | 106 +++---- R/RcppExports.R | 38 +- R/get_underlying.R | 78 ++--- R/logLike.R | 145 ++++----- R/rolling.R | 281 +++++++++---------- R/roxygen_tags.R | 6 R/utils.R | 92 +++--- build/vignette.rds |binary inst/doc/Distance-to-default.R | 218 +++++++------- inst/doc/Distance-to-default.Rnw | 527 +++++++++++++++++++----------------- inst/doc/Distance-to-default.pdf |binary man/BS_fit.Rd | 132 ++++----- man/BS_fit_rolling.Rd | 219 +++++++------- man/BS_sim.Rd | 86 ++--- man/get_underlying.Rd | 98 +++--- man/merton_ll.Rd | 132 ++++----- src/Brent_fmin.c |only src/Brent_fmin.h |only src/est_iterative.cpp | 2 src/get_underlying.cpp | 6 src/mle.cpp | 140 +++++++-- tests/testthat.R | 8 tests/testthat/test_bs.R | 136 ++++----- tests/testthat/test_est_iterative.R | 90 +++--- tests/testthat/test_logLike.R | 51 ++- tests/testthat/test_mle.R | 63 ++-- tests/testthat/test_rolling.R | 136 ++++----- tests/testthat/test_sim.R | 98 +++--- vignettes/Distance-to-default.Rnw | 527 +++++++++++++++++++----------------- vignettes/Distance-to-default.bib | 118 ++++---- 36 files changed, 2067 insertions(+), 1861 deletions(-)
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-07-23 0.1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2020-01-24 0.0.2
2019-04-01 0.0.1
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2019-04-18 1.3
2017-10-25 1.2
2017-03-08 1.1
2016-12-24 1.0
Previous versions (as known to CRANberries) which should be available via the Archive link are:
2018-10-30 0.2.2
Title: Kernel Smoothing
Description: Kernel smoothers for univariate and multivariate data, including densities, density derivatives, cumulative distributions, clustering, classification, density ridges, significant modal regions, and two-sample hypothesis tests. Chacon & Duong (2018) <doi:10.1201/9780429485572>.
Author: Tarn Duong [aut, cre],
Matt Wand [ctb],
Jose Chacon [ctb],
Artur Gramacki [ctb]
Maintainer: Tarn Duong <tarn.duong@gmail.com>
Diff between ks versions 1.11.6 dated 2019-11-04 and 1.11.7 dated 2020-02-11
CHANGELOG | 3 +++ DESCRIPTION | 8 ++++---- MD5 | 18 +++++++++--------- NAMESPACE | 1 + R/selector.R | 2 ++ build/vignette.rds |binary inst/doc/kde.pdf |binary man/Hnm.Rd | 4 ++-- man/kde.truncate.Rd | 1 - man/kdr.Rd | 1 - 10 files changed, 21 insertions(+), 17 deletions(-)
Title: Generalized Mann-Whitney Type Tests
Description: Generalized Mann-Whitney type tests based on probabilistic
indices and new diagnostic plots.
Author: Daniel Fischer , Hannu Oja
Maintainer: Daniel Fischer <daniel.fischer@luke.fi>
Diff between gMWT versions 1.1 dated 2016-08-17 and 1.1.1 dated 2020-02-11
DESCRIPTION | 8 ++-- MD5 | 15 ++++---- NAMESPACE | 5 +- R/getSigTests.R | 4 +- R/gmw.R | 2 - R/triple.gmw.R | 56 ++++++++++++++++++++++++++++++ inst/ChangeLog | 81 ++++++++++++++++++++++---------------------- man/gMWT-package.Rd | 4 +- src/registerDynamicSymbol.c |only 9 files changed, 118 insertions(+), 57 deletions(-)
Title: Global Envelopes
Description: Implementation of global envelopes for a set of general d-dimensional vectors T in various applications. A 100(1-alpha)% global envelope is a band bounded by two vectors such that the probability that T falls outside this envelope in any of the d points is equal to alpha. Global means that the probability is controlled simultaneously for all the d elements of the vectors. The global envelopes can be used for graphical Monte Carlo and permutation tests where the test statistic is a multivariate vector or function (e.g. goodness-of-fit testing for point patterns and random sets, functional analysis of variance, functional general linear model, n-sample test of correspondence of distribution functions), for central regions of functional or multivariate data (e.g. outlier detection, functional boxplot) and for global confidence and prediction bands (e.g. confidence band in polynomial regression, Bayesian posterior prediction). See Myllymäki and Mrkvička (2019) <arXiv:1911.06583>, Myllymäki et al. (2017) <doi: 10.1111/rssb.12172>, Mrkvička et al. (2017) <doi: 10.1007/s11222-016-9683-9>, Mrkvička et al. (2016) <doi: 10.1016/j.spasta.2016.04.005>, Mrkvička et al. (2018) <arXiv:1612.03608>, Mrkvička et al. (2019) <arXiv:1906.09004>, Mrkvička et al. (2019) <arXiv:1902.04926>.
Author: Mari Myllymäki [aut, cre],
Tomáš Mrkvička [aut],
Pavel Grabarnik [ctb],
Ute Hahn [ctb],
Mikko Kuronen [ctb],
Michael Rost [ctb],
Henri Seijo [ctb]
Maintainer: Mari Myllymäki <mari.myllymaki@luke.fi>
Diff between GET versions 0.1-4 dated 2019-11-21 and 0.1-5 dated 2020-02-11
DESCRIPTION | 12 MD5 | 127 ++-- NAMESPACE | 3 R/GET-package.r | 1 R/abide_9002_23.r |only R/adjusted_envelopes.r | 198 ++----- R/envelopes.r | 46 + R/envelopes2d.r | 59 -- R/image_set.r | 45 + R/plot_envelope_helper.R | 40 + R/saplings.r | 6 data/abide_9002_23.RData |only data/datalist | 1 man/GDPtax.Rd | 114 ++-- man/GET-package.Rd | 581 +++++++++++----------- man/GET.composite.Rd | 643 +++++++++++------------- man/GET.necdf.Rd | 195 +++---- man/GET.variogram.Rd | 172 +++--- man/abide_9002_23.Rd |only man/adult_trees.Rd | 62 +- man/central_region.Rd | 479 +++++++++--------- man/central_region2d.Rd | 82 +-- man/cgec.Rd | 122 ++-- man/combined_scaled_MAD_envelope.Rd | 202 ++++--- man/create_curve_set.Rd | 62 +- man/create_image_set.Rd | 79 +-- man/crop_curves.Rd | 52 +- man/deviation_test.Rd | 224 ++++---- man/envelope_to_curve_set.Rd | 40 - man/fBoxplot.Rd | 82 +-- man/fallen_trees.Rd | 74 +- man/forder.Rd | 267 +++++----- man/frank.fanova.Rd | 155 +++--- man/frank.fanova2d.Rd | 84 +-- man/frank.flm.Rd | 251 +++++---- man/frank.flm2d.Rd | 136 ++--- man/global_envelope_test.Rd | 824 ++++++++++++++++---------------- man/global_envelope_test2d.Rd | 192 +++---- man/graph.fanova.Rd | 452 ++++++++--------- man/graph.fanova2d.Rd | 100 +-- man/graph.flm.Rd | 293 +++++------ man/graph.flm2d.Rd | 160 +++--- man/imageset1.Rd | 88 +-- man/imageset2.Rd | 86 +-- man/imageset3.Rd | 82 +-- man/is.curve_set.Rd | 28 - man/plot.combined_fboxplot.Rd | 53 +- man/plot.combined_global_envelope.Rd | 150 +++-- man/plot.combined_global_envelope2d.Rd | 98 ++- man/plot.curve_set.Rd | 77 +- man/plot.fboxplot.Rd | 76 +- man/plot.global_envelope.Rd | 142 +++-- man/plot.global_envelope2d.Rd | 90 +-- man/plot.image_set.Rd | 71 +- man/print.combined_global_envelope.Rd | 32 - man/print.combined_global_envelope2d.Rd | 32 - man/print.curve_set.Rd | 32 - man/print.deviation_test.Rd | 32 - man/print.global_envelope.Rd | 32 - man/print.global_envelope2d.Rd | 32 - man/print.image_set.Rd | 32 - man/qdir_envelope.Rd | 174 +++--- man/rank_envelope.Rd | 192 +++---- man/residual.Rd | 74 +- man/rimov.Rd | 84 +-- man/saplings.Rd | 234 ++++----- 66 files changed, 4433 insertions(+), 4307 deletions(-)
Title: Bayesian ANOVA
Description: Provides a Bayesian version of the analysis of variance based on a three-component Gaussian mixture for which a Gibbs sampler produces posterior draws. For details about the Bayesian ANOVA based on Gaussian mixtures, see Kelter (2019) <arXiv:1906.07524>.
Author: Riko Kelter
Maintainer: Riko Kelter <riko.kelter@uni-siegen.de>
Diff between bayesanova versions 1.2 dated 2019-11-25 and 1.3 dated 2020-02-11
bayesanova-1.2/bayesanova/man/post.fit.Rd |only bayesanova-1.3/bayesanova/DESCRIPTION | 8 - bayesanova-1.3/bayesanova/MD5 | 10 +- bayesanova-1.3/bayesanova/NAMESPACE | 3 bayesanova-1.3/bayesanova/R/bayes.anova.R | 96 ++++++++++++----------- bayesanova-1.3/bayesanova/build/partial.rdb |binary bayesanova-1.3/bayesanova/man/post.pred.check.Rd |only 7 files changed, 63 insertions(+), 54 deletions(-)
Title: Simulation of in Silico Multi-Omic Networks
Description: A tool for the simulation of gene expression profiles for in silico regulatory networks. The package generates gene regulatory networks, which include protein-coding and noncoding genes linked via different types of regulation: regulation of transcription, translation, RNA or protein decay, and post-translational modifications. The effect of genetic mutations on the system behaviour is accounted for via the simulation of genetically different in silico individuals. The ploidy of the system is not restricted to the usual haploid or diploid situations, but is defined by the user. A choice of stochastic simulation algorithms allow us to simulate the expression profiles (RNA and if applicable protein abundance) of the genes in the in silico system for the different in silico individuals. A tutorial explaining how to use the package is available at <https://oliviaab.github.io/sismonr/>. Manuscript in preparation; see also Angelin-Bonnet O., Biggs P.J. and Vignes M. (2018) <doi:10.1109/BIBM.2018.8621131>. Note that sismonr relies on Julia code called internally by the functions. No knowledge of Julia is required in order to use sismonr, but Julia must be installed on the computer (instructions can be found in the tutorial, the GitHub page or the vignette of the package).
Author: Olivia Angelin-Bonnet [aut, cre]
(<https://orcid.org/0000-0002-7708-2919>),
Patrick Biggs [aut] (<https://orcid.org/0000-0002-0285-4101>),
Matthieu Vignes [aut] (<https://orcid.org/0000-0001-8929-2975>),
John M. Chambers [ctb]
Maintainer: Olivia Angelin-Bonnet <olivia.angelinbonnet@gmail.com>
Diff between sismonr versions 2.0.0 dated 2019-12-12 and 2.1.0 dated 2020-02-11
DESCRIPTION | 8 - MD5 | 54 ++++++------ NEWS.md | 8 + R/stochastic_simulation.R | 110 ++++++++++++++++--------- build/vignette.rds |binary inst/doc/sismonr_vignette.html | 4 inst/julia/stochastic_simulation.jl | 34 +++++++ inst/julia/testModules.jl | 6 + man/addComplex.Rd | 8 + man/addEdge.Rd | 3 man/addGene.Rd | 11 ++ man/callJuliaStochasticSimulation.Rd | 18 +++- man/createInSilicoPopulation.Rd | 11 ++ man/createIndividual.Rd | 10 +- man/createRegulatoryNetwork.Rd | 9 +- man/createStochSystem.Rd | 10 +- man/getRNAseqMatrix.Rd | 20 +++- man/insilicoindividualargs.Rd | 11 +- man/insilicosystemargs.Rd | 120 +++++++++++++++++++--------- man/plotGRN.Rd | 9 +- man/plotHeatMap.Rd | 20 +++- man/plotMutations.Rd | 9 +- man/plotSimulation.Rd | 20 +++- man/sampleLibrarySize.Rd | 11 +- man/simulateInSilicoSystem.Rd | 69 ++++++++++------ man/simulateParallelInSilicoSystem.Rd | 81 ++++++++++++------ man/summariseSimulation.Rd | 15 ++- tests/testthat/test-stochastic_simulation.R | 2 28 files changed, 478 insertions(+), 213 deletions(-)
Title: Parallel Bayesian Optimization of Hyperparameters
Description: Fast, flexible framework for implementing Bayesian optimization of model
hyperparameters according to the methods described in Snoek et al. <arXiv:1206.2944>.
The package allows the user to run scoring function in parallel, save intermediary
results, and tweak other aspects of the process to fully utilize the computing resources
available to the user.
Author: Samuel Wilson [aut, cre]
Maintainer: Samuel Wilson <samwilson303@gmail.com>
Diff between ParBayesianOptimization versions 0.2.0 dated 2019-10-22 and 1.0.0 dated 2020-02-11
ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/multiParameterSampling.R |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/multiParameterSampling.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/multiParameterSampling.html |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/runningInParallel.R |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/runningInParallel.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/runningInParallel.html |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/savingProgress.R |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/savingProgress.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/savingProgress.html |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/standardFeatures.R |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/standardFeatures.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/standardFeatures.html |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/whenToStop.R |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/whenToStop.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/inst/doc/whenToStop.html |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/applyNoise.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/assignKern.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/checkBounds.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/checkDup.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/minMaxScale.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/randParams.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/unMMScale.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/man/zeroOneScale.Rd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/GPround1.png |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/GPround2.png |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/multiParameterSampling.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/noiseAdd.png |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/progressPlot.png |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/runningInParallel.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/savingProgress.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/slideToPic.png |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/standardFeatures.Rmd |only ParBayesianOptimization-0.2.0/ParBayesianOptimization/vignettes/whenToStop.Rmd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/DESCRIPTION | 12 ParBayesianOptimization-1.0.0/ParBayesianOptimization/MD5 | 104 +- ParBayesianOptimization-1.0.0/ParBayesianOptimization/NAMESPACE | 33 ParBayesianOptimization-1.0.0/ParBayesianOptimization/NEWS.md | 3 ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/BayesianOptimization.R | 191 +--- ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/addIterations.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/applyCluster.R | 9 ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/applyNoise.R | 49 - ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/bayesOpt.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/calcAcq.R | 12 ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/changeSaveFile.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/getBestPars.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/getLocalOptimums.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/getNextParameters.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/maxAcq.R | 23 ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/plot.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/print.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/smallFuncs.R | 142 +-- ParBayesianOptimization-1.0.0/ParBayesianOptimization/R/updateGP.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/README.md | 417 ++++++---- ParBayesianOptimization-1.0.0/ParBayesianOptimization/build/vignette.rds |binary ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/functionMaximization.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/functionMaximization.Rmd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/functionMaximization.html |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/multiPointSampling.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/multiPointSampling.Rmd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/multiPointSampling.html |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/tuningHyperparameters.R |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/tuningHyperparameters.Rmd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/inst/doc/tuningHyperparameters.html |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/BayesianOptimization.Rd | 405 ++++----- ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/addIterations.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/applyCluster.Rd | 37 ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/bayesOpt.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/calcAcq.Rd | 60 - ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/changeSaveFile.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/figures |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/getBestPars.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/getLocalOptimums.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/maxAcq.Rd | 80 + ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/plot.bayesOpt.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/plotProg.Rd | 38 ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/print.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/man/updateGP.Rd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/tests |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/vignettes/functionMaximization.Rmd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/vignettes/gpParBayesAnimationSmall.gif |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/vignettes/multiPointSampling.Rmd |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/vignettes/round1.png |only ParBayesianOptimization-1.0.0/ParBayesianOptimization/vignettes/tuningHyperparameters.Rmd |only 83 files changed, 819 insertions(+), 796 deletions(-)
More information about ParBayesianOptimization at CRAN
Permanent link