diff --git a/DESCRIPTION b/DESCRIPTION index e76b04bf..a2414dc3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -65,9 +65,9 @@ Suggests: survival, testthat (>= 3.0.0), vdiffr (>= 1.0.2) -RoxygenNote: 7.3.3 VignetteBuilder: knitr Encoding: UTF-8 Roxygen: list(markdown = TRUE) Config/testthat/edition: 3 Additional_repositories: https://stan-dev.r-universe.dev/ +Config/roxygen2/version: 8.0.0 diff --git a/R/ppc-discrete.R b/R/ppc-discrete.R index 2fc117a3..743d4a13 100644 --- a/R/ppc-discrete.R +++ b/R/ppc-discrete.R @@ -359,9 +359,9 @@ ppc_rootogram <- function(y, reduce_legend_spacing(0.25) + scale_shape_manual(values = c("In" = 22, "Out" = 23, "y" = 22), guide = "legend", labels = c("y" = expression(italic(y)))) if (bound_distinct) { - graph <- graph + guides(shape = guide_legend(expression(italic(y)~within~bounds))) + graph <- graph + guides(shape = guide_legend(expression(italic(y)~within~bounds), order = 1)) } else { - graph <- graph + guides(shape = guide_legend(" ")) + graph <- graph + guides(shape = guide_legend(" ", order = 1)) } } else { graph <- graph + @@ -374,6 +374,7 @@ ppc_rootogram <- function(y, ) + scale_fill_manual("", values = get_color("l")) + scale_color_manual("", values = get_color("dh")) + + guides(fill = guide_legend(order = 1)) + labs(x = expression(italic(y)), y = expression(sqrt(Count))) + bayesplot_theme_get() + reduce_legend_spacing(0.25) diff --git a/man/MCMC-combos.Rd b/man/MCMC-combos.Rd index 9f4e1485..86d9f87e 100644 --- a/man/MCMC-combos.Rd +++ b/man/MCMC-combos.Rd @@ -82,7 +82,7 @@ mcmc_combo( } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, \code{\link{MCMC-intervals}}, diff --git a/man/MCMC-diagnostics.Rd b/man/MCMC-diagnostics.Rd index f6dbad81..3326f11e 100644 --- a/man/MCMC-diagnostics.Rd +++ b/man/MCMC-diagnostics.Rd @@ -50,12 +50,12 @@ mcmc_acf_bar( \item{size}{Optional values to override \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}}'s default size (for \code{mcmc_rhat()}, \code{mcmc_neff()}) or -\code{\link[ggplot2:geom_path]{ggplot2::geom_line()}}'s default line width (for \code{mcmc_acf()}).} +\code{\link[ggplot2:geom_line]{ggplot2::geom_line()}}'s default line width (for \code{mcmc_acf()}).} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -85,7 +85,7 @@ similar functions. Examples of using \code{pars} in this way can be found on the \item{regex_pars}{An optional \link[base:grep]{regular expression} to use for parameter selection. Can be specified instead of \code{pars} or in addition to \code{pars}. When using \code{pars} for tidy parameter selection, the \code{regex_pars} -argument is ignored since \link[tidyselect:language]{select helpers} +argument is ignored since \link[tidyselect:select_helpers]{select helpers} perform a similar function.} \item{facet_args}{A named list of arguments (other than \code{facets}) passed @@ -229,7 +229,7 @@ vignette. using the No-U-Turn-Sampler. } -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-distributions}}, \code{\link{MCMC-intervals}}, diff --git a/man/MCMC-distributions.Rd b/man/MCMC-distributions.Rd index bfddd876..779ce9f9 100644 --- a/man/MCMC-distributions.Rd +++ b/man/MCMC-distributions.Rd @@ -155,7 +155,7 @@ similar functions. Examples of using \code{pars} in this way can be found on the \item{regex_pars}{An optional \link[base:grep]{regular expression} to use for parameter selection. Can be specified instead of \code{pars} or in addition to \code{pars}. When using \code{pars} for tidy parameter selection, the \code{regex_pars} -argument is ignored since \link[tidyselect:language]{select helpers} +argument is ignored since \link[tidyselect:select_helpers]{select helpers} perform a similar function.} \item{transformations}{Optionally, transformations to apply to parameters @@ -188,10 +188,10 @@ to control faceting. Note: if \code{scales} is not included in \code{facet_args} then \strong{bayesplot} may use \code{scales="free"} as the default (depending on the plot) instead of the \strong{ggplot2} default of \code{scales="fixed"}.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -208,7 +208,7 @@ function.)} \item{trim}{A logical scalar passed to \code{\link[ggplot2:geom_density]{ggplot2::geom_density()}}.} \item{bw, adjust, kernel, n_dens, bounds}{Optional arguments passed to -\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:geom_density]{ggplot2::stat_density()}}) to override +\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:stat_density]{ggplot2::stat_density()}}) to override default kernel density estimation parameters or truncate the density support. If \code{NULL} (default), \code{bw} is set to \code{"nrd0"}, \code{adjust} to \code{1}, \code{kernel} to \code{"gaussian"}, and \code{n_dens} to \code{1024}.} @@ -352,7 +352,7 @@ mcmc_dots_by_chain(x, regex_pars = "beta", facet_args = list(labeller = chain_la } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-intervals}}, diff --git a/man/MCMC-intervals.Rd b/man/MCMC-intervals.Rd index b17e851a..a300826e 100644 --- a/man/MCMC-intervals.Rd +++ b/man/MCMC-intervals.Rd @@ -126,7 +126,7 @@ similar functions. Examples of using \code{pars} in this way can be found on the \item{regex_pars}{An optional \link[base:grep]{regular expression} to use for parameter selection. Can be specified instead of \code{pars} or in addition to \code{pars}. When using \code{pars} for tidy parameter selection, the \code{regex_pars} -argument is ignored since \link[tidyselect:language]{select helpers} +argument is ignored since \link[tidyselect:select_helpers]{select helpers} perform a similar function.} \item{transformations}{Optionally, transformations to apply to parameters @@ -184,7 +184,7 @@ points across the curves are the same height. The method \code{"scaled height"} the ridgelines.} \item{bw, adjust, kernel, n_dens, bounds}{Optional arguments passed to -\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:geom_density]{ggplot2::stat_density()}}) to override +\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:stat_density]{ggplot2::stat_density()}}) to override default kernel density estimation parameters or truncate the density support. If \code{NULL} (default), \code{bw} is set to \code{"nrd0"}, \code{adjust} to \code{1}, \code{kernel} to \code{"gaussian"}, and \code{n_dens} to \code{1024}.} @@ -358,7 +358,7 @@ mcmc_areas_ridges(m, pars = "mu", regex_pars = "theta", border_size = 0.75) + } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, diff --git a/man/MCMC-nuts.Rd b/man/MCMC-nuts.Rd index 4a2d7273..c8c2b7b4 100644 --- a/man/MCMC-nuts.Rd +++ b/man/MCMC-nuts.Rd @@ -56,10 +56,10 @@ selected chain. The \code{chain} argument is not used by \code{mcmc_nuts_energy( \item{...}{Currently ignored.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -207,7 +207,7 @@ corresponding divergences and/or max treedepth saturation. } } -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, diff --git a/man/MCMC-overview.Rd b/man/MCMC-overview.Rd index eed5117f..61f67240 100644 --- a/man/MCMC-overview.Rd +++ b/man/MCMC-overview.Rd @@ -72,7 +72,7 @@ Gelman, A. (2019), Visualization in Bayesian workflow. \href{https://github.com/jgabry/bayes-vis-paper}{code on GitHub}) } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, diff --git a/man/MCMC-parcoord.Rd b/man/MCMC-parcoord.Rd index cbb7d294..182a7be7 100644 --- a/man/MCMC-parcoord.Rd +++ b/man/MCMC-parcoord.Rd @@ -51,7 +51,7 @@ similar functions. Examples of using \code{pars} in this way can be found on the \item{regex_pars}{An optional \link[base:grep]{regular expression} to use for parameter selection. Can be specified instead of \code{pars} or in addition to \code{pars}. When using \code{pars} for tidy parameter selection, the \code{regex_pars} -argument is ignored since \link[tidyselect:language]{select helpers} +argument is ignored since \link[tidyselect:select_helpers]{select helpers} perform a similar function.} \item{transformations}{Optionally, transformations to apply to parameters @@ -78,7 +78,7 @@ abbreviated for convenience in interactive use (e.g., \code{transform}).} \item{...}{Currently ignored.} -\item{size, alpha}{Arguments passed on to \code{\link[ggplot2:geom_path]{ggplot2::geom_line()}}.} +\item{size, alpha}{Arguments passed on to \code{\link[ggplot2:geom_line]{ggplot2::geom_line()}}.} \item{np}{For models fit using \link{NUTS} (more generally, any \href{https://en.wikipedia.org/wiki/Symplectic_integrator}{symplectic integrator}), @@ -93,7 +93,7 @@ argument is specified.} \item{div_color, div_size, div_alpha}{Optional arguments to the \code{parcoord_style_np()} helper function that are eventually passed to -\code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} if the \code{np} argument is also specified. They control +\code{\link[ggplot2:geom_line]{ggplot2::geom_line()}} if the \code{np} argument is also specified. They control the color, size, and transparency specifications for showing divergences in the plot. The default values are displayed in the \strong{Usage} section above.} } @@ -197,7 +197,7 @@ Hartikainen, A. (2017, Aug 23). Concentration of divergences \url{https://discourse.mc-stan.org/t/concentration-of-divergences/1590/21}. } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, diff --git a/man/MCMC-recover.Rd b/man/MCMC-recover.Rd index 1a46095c..473c172d 100644 --- a/man/MCMC-recover.Rd +++ b/man/MCMC-recover.Rd @@ -87,10 +87,10 @@ default), \code{"mean"}, or \code{"none"}.} \item{size, alpha}{Passed to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}} to control the appearance of plotted points.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -166,7 +166,7 @@ mcmc_recover_hist(draws[, 1:4], true[1:4]) } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, diff --git a/man/MCMC-scatterplots.Rd b/man/MCMC-scatterplots.Rd index ce4fa7f0..060fb14f 100644 --- a/man/MCMC-scatterplots.Rd +++ b/man/MCMC-scatterplots.Rd @@ -94,7 +94,7 @@ similar functions. Examples of using \code{pars} in this way can be found on the \item{regex_pars}{An optional \link[base:grep]{regular expression} to use for parameter selection. Can be specified instead of \code{pars} or in addition to \code{pars}. When using \code{pars} for tidy parameter selection, the \code{regex_pars} -argument is ignored since \link[tidyselect:language]{select helpers} +argument is ignored since \link[tidyselect:select_helpers]{select helpers} perform a similar function.} \item{transformations}{Optionally, transformations to apply to parameters @@ -415,7 +415,7 @@ Gelman, A. (2019), Visualization in Bayesian workflow. \href{https://github.com/jgabry/bayes-vis-paper}{code on GitHub}) } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, diff --git a/man/MCMC-traces.Rd b/man/MCMC-traces.Rd index 52cb6da3..ff30246c 100644 --- a/man/MCMC-traces.Rd +++ b/man/MCMC-traces.Rd @@ -111,7 +111,7 @@ similar functions. Examples of using \code{pars} in this way can be found on the \item{regex_pars}{An optional \link[base:grep]{regular expression} to use for parameter selection. Can be specified instead of \code{pars} or in addition to \code{pars}. When using \code{pars} for tidy parameter selection, the \code{regex_pars} -argument is ignored since \link[tidyselect:language]{select helpers} +argument is ignored since \link[tidyselect:select_helpers]{select helpers} perform a similar function.} \item{transformations}{Optionally, transformations to apply to parameters @@ -368,7 +368,7 @@ Säilynoja, T., Bürkner, P., Vehtari, A. Goodness of Fit Evaluation and Multiple Sample Comparison \href{https://arxiv.org/abs/2103.10522}{arXiv preprint}. } \seealso{ -Other MCMC: +Other MCMC: \code{\link{MCMC-combos}}, \code{\link{MCMC-diagnostics}}, \code{\link{MCMC-distributions}}, diff --git a/man/PPC-censoring.Rd b/man/PPC-censoring.Rd index 68026b20..c5b2baff 100644 --- a/man/PPC-censoring.Rd +++ b/man/PPC-censoring.Rd @@ -150,7 +150,7 @@ from incomplete observations. doi:10.1080/01621459.1958.10501452. } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-discrete}}, \code{\link{PPC-distributions}}, \code{\link{PPC-errors}}, diff --git a/man/PPC-discrete.Rd b/man/PPC-discrete.Rd index 5f832a78..986f88bb 100644 --- a/man/PPC-discrete.Rd +++ b/man/PPC-discrete.Rd @@ -82,9 +82,9 @@ of the expected counts.)} the bar width.} \item{size, fatten, linewidth}{For bar plots, \code{size}, \code{fatten}, and \code{linewidth} -are passed to \code{\link[ggplot2:geom_linerange]{ggplot2::geom_pointrange()}} to control the appearance of the +are passed to \code{\link[ggplot2:geom_pointrange]{ggplot2::geom_pointrange()}} to control the appearance of the \code{yrep} points and intervals. For rootograms \code{size} is passed to -\code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} and \code{\link[ggplot2:geom_linerange]{ggplot2::geom_pointrange()}}.} +\code{\link[ggplot2:geom_line]{ggplot2::geom_line()}} and \code{\link[ggplot2:geom_pointrange]{ggplot2::geom_pointrange()}}.} \item{freq}{For bar plots only, if \code{TRUE} (the default) the y-axis will display counts. Setting \code{freq=FALSE} will put proportions on the y-axis.} @@ -281,7 +281,7 @@ Visualizing count data regressions using rootograms. \url{https://arxiv.org/abs/1605.01311}. } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-distributions}}, \code{\link{PPC-errors}}, diff --git a/man/PPC-distributions.Rd b/man/PPC-distributions.Rd index 02a4d698..f58512e9 100644 --- a/man/PPC-distributions.Rd +++ b/man/PPC-distributions.Rd @@ -187,7 +187,7 @@ the predictive distributions.} \item{trim}{A logical scalar passed to \code{\link[ggplot2:geom_density]{ggplot2::geom_density()}}.} \item{bw, adjust, kernel, n_dens, bounds}{Optional arguments passed to -\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:geom_density]{ggplot2::stat_density()}}) to override +\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:stat_density]{ggplot2::stat_density()}}) to override default kernel density estimation parameters or truncate the density support. If \code{NULL} (default), \code{bw} is set to \code{"nrd0"}, \code{adjust} to \code{1}, \code{kernel} to \code{"gaussian"}, and \code{n_dens} to \code{1024}.} @@ -198,10 +198,10 @@ now always used.} \item{pad}{A logical scalar passed to \code{\link[ggplot2:stat_ecdf]{ggplot2::stat_ecdf()}}.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -465,7 +465,7 @@ Tesso, H., & Vehtari, A. (2026). LOO-PIT predictive model checking. arXiv preprint https://arxiv.org/abs/2603.02928. } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-discrete}}, \code{\link{PPC-errors}}, diff --git a/man/PPC-errors.Rd b/man/PPC-errors.Rd index f3931c26..f8cba214 100644 --- a/man/PPC-errors.Rd +++ b/man/PPC-errors.Rd @@ -101,7 +101,7 @@ to control faceting. Note: if \code{scales} is not included in \code{facet_args} then \strong{bayesplot} may use \code{scales="free"} as the default (depending on the plot) instead of the \strong{ggplot2} default of \code{scales="fixed"}.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} \item{bins}{For \code{ppc_error_binned()}, the number of bins to use (approximately).} @@ -250,7 +250,7 @@ A., and Rubin, D. B. (2013). \emph{Bayesian Data Analysis.} Chapman & Hall/CRC Press, London, third edition. (Ch. 6) } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-discrete}}, \code{\link{PPC-distributions}}, diff --git a/man/PPC-intervals.Rd b/man/PPC-intervals.Rd index 5b3bea32..549327e8 100644 --- a/man/PPC-intervals.Rd +++ b/man/PPC-intervals.Rd @@ -109,10 +109,10 @@ are \code{prob=0.5} and \code{prob_outer=0.9}.} \item{alpha, size, fatten, linewidth}{Arguments passed to geoms. For ribbon plots \code{alpha} is passed to \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_ribbon()}} to control the opacity -of the outer ribbon and \code{size} is passed to \code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} to +of the outer ribbon and \code{size} is passed to \code{\link[ggplot2:geom_line]{ggplot2::geom_line()}} to control the size of the line representing the median prediction (\code{size=0} will remove the line). For interval plots \code{alpha}, \code{size}, \code{fatten}, and -\code{linewidth} are passed to \code{\link[ggplot2:geom_linerange]{ggplot2::geom_pointrange()}} (\code{fatten=0} will +\code{linewidth} are passed to \code{\link[ggplot2:geom_pointrange]{ggplot2::geom_pointrange()}} (\code{fatten=0} will remove the point estimates).} \item{group}{A grouping variable of the same length as \code{y}. @@ -247,7 +247,7 @@ A., and Rubin, D. B. (2013). \emph{Bayesian Data Analysis.} Chapman & Hall/CRC Press, London, third edition. (Ch. 6) } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-discrete}}, \code{\link{PPC-distributions}}, diff --git a/man/PPC-loo.Rd b/man/PPC-loo.Rd index 9758172b..b25f5bec 100644 --- a/man/PPC-loo.Rd +++ b/man/PPC-loo.Rd @@ -155,7 +155,7 @@ PITs overlaid as a thicker dark line.} plot aesthetics. For \code{ppc_loo_pit_qq()} and \code{ppc_loo_pit_overlay()},\code{size} and \code{alpha} are passed to \code{\link[ggplot2:geom_point]{ggplot2::geom_point()}} and \code{\link[ggplot2:geom_density]{ggplot2::geom_density()}}, respectively. For \code{ppc_loo_intervals()}, \code{size} -\code{linewidth} and \code{fatten} are passed to \code{\link[ggplot2:geom_linerange]{ggplot2::geom_pointrange()}}. For +\code{linewidth} and \code{fatten} are passed to \code{\link[ggplot2:geom_pointrange]{ggplot2::geom_pointrange()}}. For \code{ppc_loo_ribbon()}, \code{alpha} and \code{size} are passed to \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_ribbon()}}. For \code{ppc_loo_pit_ecdf()}, linewidth for the ECDF plot. When \code{method = "correlated"}, defaults to 0.3. When \code{method = "independent"}, @@ -176,7 +176,7 @@ generate the estimations. This is set to 512 by default.} \item{bw, adjust, kernel, n_dens}{Optional arguments passed to \code{\link[stats:density]{stats::density()}} to override the defaults.} -\item{trim}{Passed to \code{\link[ggplot2:geom_density]{ggplot2::stat_density()}}.} +\item{trim}{Passed to \code{\link[ggplot2:stat_density]{ggplot2::stat_density()}}.} \item{compare}{For \code{ppc_loo_pit_qq()}, a string that can be either \code{"uniform"} or \code{"normal"}. If \code{"uniform"} (the default) the Q-Q plot @@ -414,7 +414,7 @@ Tesso, H., & Vehtari, A. (2026). LOO-PIT predictive model checking. arXiv preprint https://arxiv.org/abs/2603.02928. } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-discrete}}, \code{\link{PPC-distributions}}, diff --git a/man/PPC-overview.Rd b/man/PPC-overview.Rd index 16d3f0ff..e277b291 100644 --- a/man/PPC-overview.Rd +++ b/man/PPC-overview.Rd @@ -123,7 +123,7 @@ A., and Rubin, D. B. (2013). \emph{Bayesian Data Analysis.} Chapman & Hall/CRC Press, London, third edition. (Ch. 6) } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-discrete}}, \code{\link{PPC-distributions}}, diff --git a/man/PPC-scatterplots.Rd b/man/PPC-scatterplots.Rd index edec930a..c883ad94 100644 --- a/man/PPC-scatterplots.Rd +++ b/man/PPC-scatterplots.Rd @@ -163,7 +163,7 @@ A., and Rubin, D. B. (2013). \emph{Bayesian Data Analysis.} Chapman & Hall/CRC Press, London, third edition. (Ch. 6) } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-discrete}}, \code{\link{PPC-distributions}}, diff --git a/man/PPC-test-statistics.Rd b/man/PPC-test-statistics.Rd index da1c2aca..14d22c74 100644 --- a/man/PPC-test-statistics.Rd +++ b/man/PPC-test-statistics.Rd @@ -88,10 +88,10 @@ then generic naming is used in the legend.} \item{discrete}{For \code{ppc_stat()} and \code{ppc_stat_grouped()}, if \code{TRUE} then a bar chart is used instead of a histogram.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -235,7 +235,7 @@ A., and Rubin, D. B. (2013). \emph{Bayesian Data Analysis.} Chapman & Hall/CRC Press, London, third edition. (Ch. 6) } \seealso{ -Other PPCs: +Other PPCs: \code{\link{PPC-censoring}}, \code{\link{PPC-discrete}}, \code{\link{PPC-distributions}}, diff --git a/man/PPD-distributions.Rd b/man/PPD-distributions.Rd index 2f04c4b8..09604d63 100644 --- a/man/PPD-distributions.Rd +++ b/man/PPD-distributions.Rd @@ -122,7 +122,7 @@ the predictive distributions.} \item{trim}{A logical scalar passed to \code{\link[ggplot2:geom_density]{ggplot2::geom_density()}}.} \item{bw, adjust, kernel, n_dens, bounds}{Optional arguments passed to -\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:geom_density]{ggplot2::stat_density()}}) to override +\code{\link[stats:density]{stats::density()}} (and \code{bounds} to \code{\link[ggplot2:stat_density]{ggplot2::stat_density()}}) to override default kernel density estimation parameters or truncate the density support. If \code{NULL} (default), \code{bw} is set to \code{"nrd0"}, \code{adjust} to \code{1}, \code{kernel} to \code{"gaussian"}, and \code{n_dens} to \code{1024}.} @@ -133,10 +133,10 @@ now always used.} \item{pad}{A logical scalar passed to \code{\link[ggplot2:stat_ecdf]{ggplot2::stat_ecdf()}}.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -185,7 +185,7 @@ ppc_dens_overlay(y = example_y_data(), yrep = preds[1:50, ]) } \seealso{ -Other PPDs: +Other PPDs: \code{\link{PPD-intervals}}, \code{\link{PPD-overview}}, \code{\link{PPD-test-statistics}} diff --git a/man/PPD-intervals.Rd b/man/PPD-intervals.Rd index edadf8e9..af7c1add 100644 --- a/man/PPD-intervals.Rd +++ b/man/PPD-intervals.Rd @@ -96,10 +96,10 @@ are \code{prob=0.5} and \code{prob_outer=0.9}.} \item{alpha, size, fatten, linewidth}{Arguments passed to geoms. For ribbon plots \code{alpha} is passed to \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_ribbon()}} to control the opacity -of the outer ribbon and \code{size} is passed to \code{\link[ggplot2:geom_path]{ggplot2::geom_line()}} to +of the outer ribbon and \code{size} is passed to \code{\link[ggplot2:geom_line]{ggplot2::geom_line()}} to control the size of the line representing the median prediction (\code{size=0} will remove the line). For interval plots \code{alpha}, \code{size}, \code{fatten}, and -\code{linewidth} are passed to \code{\link[ggplot2:geom_linerange]{ggplot2::geom_pointrange()}} (\code{fatten=0} will +\code{linewidth} are passed to \code{\link[ggplot2:geom_pointrange]{ggplot2::geom_pointrange()}} (\code{fatten=0} will remove the point estimates).} \item{group}{A grouping variable of the same length as \code{y}. @@ -167,7 +167,7 @@ Gelman, A. (2019), Visualization in Bayesian workflow. \href{https://github.com/jgabry/bayes-vis-paper}{code on GitHub}) } \seealso{ -Other PPDs: +Other PPDs: \code{\link{PPD-distributions}}, \code{\link{PPD-overview}}, \code{\link{PPD-test-statistics}} diff --git a/man/PPD-overview.Rd b/man/PPD-overview.Rd index 5c8ec5ef..0876e4ce 100644 --- a/man/PPD-overview.Rd +++ b/man/PPD-overview.Rd @@ -45,7 +45,7 @@ Gelman, A. (2019), Visualization in Bayesian workflow. \href{https://github.com/jgabry/bayes-vis-paper}{code on GitHub}) } \seealso{ -Other PPDs: +Other PPDs: \code{\link{PPD-distributions}}, \code{\link{PPD-intervals}}, \code{\link{PPD-test-statistics}} diff --git a/man/PPD-test-statistics.Rd b/man/PPD-test-statistics.Rd index 4acc8adb..e613013a 100644 --- a/man/PPD-test-statistics.Rd +++ b/man/PPD-test-statistics.Rd @@ -92,10 +92,10 @@ then generic naming is used in the legend.} \item{discrete}{For \code{ppc_stat()} and \code{ppc_stat_grouped()}, if \code{TRUE} then a bar chart is used instead of a histogram.} -\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}}, +\item{binwidth}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}}, \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}}, and \code{\link[ggdist:stat_dots]{ggdist::stat_dots()}} to override the default binwidth.} -\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_ribbon]{ggplot2::geom_area()}} +\item{bins}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} and \code{\link[ggplot2:geom_area]{ggplot2::geom_area()}} to override the default binning.} \item{breaks}{Passed to \code{\link[ggplot2:geom_histogram]{ggplot2::geom_histogram()}} as an alternative to @@ -161,7 +161,7 @@ Gelman, A. (2019), Visualization in Bayesian workflow. \href{https://github.com/jgabry/bayes-vis-paper}{code on GitHub}) } \seealso{ -Other PPDs: +Other PPDs: \code{\link{PPD-distributions}}, \code{\link{PPD-intervals}}, \code{\link{PPD-overview}} diff --git a/man/bayesplot-colors.Rd b/man/bayesplot-colors.Rd index a6044eb4..228e1aa9 100644 --- a/man/bayesplot-colors.Rd +++ b/man/bayesplot-colors.Rd @@ -75,7 +75,7 @@ etc.). The order of \code{x} and \code{y} matters, i.e., the color schemes guarantee that every possible mixed scheme will look good with every possible plot. \item \code{"brewer-x"}, replacing \code{x} with the name of a palette available from -\code{\link[RColorBrewer:ColorBrewer]{RColorBrewer::brewer.pal()}} (e.g., \code{brewer-PuBuGn}). +\code{\link[RColorBrewer:brewer.pal]{RColorBrewer::brewer.pal()}} (e.g., \code{brewer-PuBuGn}). } If you have a suggestion for a new color scheme please let us know via the diff --git a/man/bayesplot-extractors.Rd b/man/bayesplot-extractors.Rd index 593a2b0e..b638f1b9 100644 --- a/man/bayesplot-extractors.Rd +++ b/man/bayesplot-extractors.Rd @@ -70,7 +70,7 @@ model parameters. If \code{pars} is omitted all parameters are included.} \item{regex_pars}{An optional \link[base:grep]{regular expression} to use for parameter selection. Can be specified instead of \code{pars} or in addition to \code{pars}. When using \code{pars} for tidy parameter selection, the \code{regex_pars} -argument is ignored since \link[tidyselect:language]{select helpers} +argument is ignored since \link[tidyselect:select_helpers]{select helpers} perform a similar function.} } \value{ diff --git a/man/bayesplot-helpers.Rd b/man/bayesplot-helpers.Rd index 460511d0..7a065e3d 100644 --- a/man/bayesplot-helpers.Rd +++ b/man/bayesplot-helpers.Rd @@ -76,24 +76,24 @@ the first argument to \code{fun}.} vector.} \item{...}{For the various \code{vline_}, \code{hline_}, and \code{abline_} -functions, \code{...} is passed to \code{\link[ggplot2:geom_abline]{ggplot2::geom_vline()}}, -\code{\link[ggplot2:geom_abline]{ggplot2::geom_hline()}}, and \code{\link[ggplot2:geom_abline]{ggplot2::geom_abline()}}, +functions, \code{...} is passed to \code{\link[ggplot2:geom_vline]{ggplot2::geom_vline()}}, +\code{\link[ggplot2:geom_hline]{ggplot2::geom_hline()}}, and \code{\link[ggplot2:geom_abline]{ggplot2::geom_abline()}}, respectively, to control the appearance of the line(s). For functions ending in \verb{_bg}, \code{...} is passed to -\code{\link[ggplot2:element]{ggplot2::element_rect()}}. +\code{\link[ggplot2:element_rect]{ggplot2::element_rect()}}. For functions ending in \verb{_text} or \verb{_title}, \code{...} is passed -to \code{\link[ggplot2:element]{ggplot2::element_text()}}. +to \code{\link[ggplot2:element_text]{ggplot2::element_text()}}. For \code{xaxis_ticks} and \code{yaxis_ticks}, \code{...} is passed to -\code{\link[ggplot2:element]{ggplot2::element_line()}}. +\code{\link[ggplot2:element_line]{ggplot2::element_line()}}. For \code{overlay_function}, \code{...} is passed to -\code{\link[ggplot2:geom_function]{ggplot2::stat_function()}}.} +\code{\link[ggplot2:stat_function]{ggplot2::stat_function()}}.} \item{na.rm}{A logical scalar passed to the appropriate geom (e.g. -\code{\link[ggplot2:geom_abline]{ggplot2::geom_vline()}}). The default is \code{TRUE}.} +\code{\link[ggplot2:geom_vline]{ggplot2::geom_vline()}}). The default is \code{TRUE}.} \item{p}{The probability mass (in \verb{[0,1]}) to include in the interval.} @@ -107,12 +107,12 @@ or a string among \code{"right"}, \code{"left"}, \code{"top"}, equivalent to using \code{legend_none()}.} \item{on}{For functions modifying ggplot \link[ggplot2:theme]{theme} elements, -set \code{on=FALSE} to set the element to \code{\link[ggplot2:element]{ggplot2::element_blank()}}. For +set \code{on=FALSE} to set the element to \code{\link[ggplot2:element_blank]{ggplot2::element_blank()}}. For example, facet text can be removed by adding \code{facet_text(on=FALSE)}, or simply \code{facet_text(FALSE)} to a ggplot object. If \code{on=TRUE} (the default), then \code{...} can be used to customize the appearance of the theme element.} -\item{color, linewidth}{Passed to \code{\link[ggplot2:element]{ggplot2::element_line()}}.} +\item{color, linewidth}{Passed to \code{\link[ggplot2:element_line]{ggplot2::element_line()}}.} \item{size}{\ifelse{html}{\href{https://lifecycle.r-lib.org/articles/stages.html#deprecated}{\figure{lifecycle-deprecated.svg}{options: alt='[Deprecated]'}}}{\strong{[Deprecated]}} Use \code{linewidth} instead.} } @@ -130,7 +130,7 @@ Convenience functions for adding to (and changing details of) ggplot objects \subsection{Add vertical, horizontal, and diagonal lines to plots}{ \itemize{ \item \code{vline_at()} and \code{hline_at()} return an object created by either -\code{\link[ggplot2:geom_abline]{ggplot2::geom_vline()}} or \code{\link[ggplot2:geom_abline]{ggplot2::geom_hline()}} that can be added to a +\code{\link[ggplot2:geom_vline]{ggplot2::geom_vline()}} or \code{\link[ggplot2:geom_hline]{ggplot2::geom_hline()}} that can be added to a ggplot object to draw a vertical or horizontal line (at one or several values). If \code{fun} is missing then the lines are drawn at the values in \code{v}. If \code{fun} is specified then the lines are drawn at the values returned by \code{fun(v)}. @@ -191,7 +191,7 @@ an existing plot (ggplot object) to add grid lines to the plot background. \subsection{Superimpose a function on an existing plot}{ \itemize{ -\item \code{overlay_function()} is a simple wrapper for \code{\link[ggplot2:geom_function]{ggplot2::stat_function()}} but +\item \code{overlay_function()} is a simple wrapper for \code{\link[ggplot2:stat_function]{ggplot2::stat_function()}} but with the \code{inherit.aes} argument fixed to \code{FALSE}. Fixing \code{inherit.aes=FALSE} will avoid potential errors due to the \code{\link[ggplot2:aes]{ggplot2::aes()}}thetic mapping used by certain \strong{bayesplot} plotting functions. diff --git a/man/bayesplot-package.Rd b/man/bayesplot-package.Rd index b35bbfa3..06553cf0 100644 --- a/man/bayesplot-package.Rd +++ b/man/bayesplot-package.Rd @@ -119,6 +119,7 @@ for plotting. Authors: \itemize{ + \item Jonah Gabry \email{jgabry@gmail.com} \item Tristan Mahr (\href{https://orcid.org/0000-0002-8890-5116}{ORCID}) } diff --git a/man/bayesplot_theme_get.Rd b/man/bayesplot_theme_get.Rd index a3dbed16..375a8efa 100644 --- a/man/bayesplot_theme_get.Rd +++ b/man/bayesplot_theme_get.Rd @@ -17,7 +17,7 @@ bayesplot_theme_replace(...) } \arguments{ \item{new}{The new theme (list of theme elements) to use. This is analogous -to the \code{new} argument to \code{\link[ggplot2:get_theme]{ggplot2::theme_set()}}.} +to the \code{new} argument to \code{\link[ggplot2:theme_set]{ggplot2::theme_set()}}.} \item{...}{A named list of theme settings.} } @@ -29,7 +29,7 @@ the \strong{ggplot2} versions of these functions. } \description{ These functions are the \strong{bayesplot} equivalent to -\strong{ggplot2}'s \code{\link[ggplot2:get_theme]{ggplot2::theme_set()}} and friends. They set, get, and update +\strong{ggplot2}'s \code{\link[ggplot2:theme_set]{ggplot2::theme_set()}} and friends. They set, get, and update the active theme but only apply them to \code{bayesplots}. The current/active theme is automatically applied to every \code{bayesplot} you draw. @@ -39,9 +39,9 @@ Use \code{bayesplot_theme_get()} to get the current \strong{bayesplot} theme and } \details{ \code{bayesplot_theme_set()} and friends only apply to \code{bayesplots}. -However, \code{\link[ggplot2:get_theme]{ggplot2::theme_set()}} can also be used to change the +However, \code{\link[ggplot2:theme_set]{ggplot2::theme_set()}} can also be used to change the \strong{bayesplot} theme. Currently, setting a theme with \code{ggplot2::theme_set()} -(other than the \strong{ggplot2} default \code{\link[ggplot2:ggtheme]{ggplot2::theme_grey()}}) will override +(other than the \strong{ggplot2} default \code{\link[ggplot2:theme_grey]{ggplot2::theme_grey()}}) will override the \strong{bayesplot} theme. } \examples{ diff --git a/man/reexports.Rd b/man/reexports.Rd index 2cd7447c..d17ac5c0 100644 --- a/man/reexports.Rd +++ b/man/reexports.Rd @@ -11,6 +11,6 @@ These objects are imported from other packages. Follow the links below to see their documentation. \describe{ - \item{dplyr}{\code{\link[dplyr]{vars}}} + \item{dplyr}{\code{\link[dplyr:vars]{vars()}}} }} diff --git a/man/theme_default.Rd b/man/theme_default.Rd index 37ae1112..4216a2c0 100644 --- a/man/theme_default.Rd +++ b/man/theme_default.Rd @@ -11,7 +11,7 @@ theme_default( } \arguments{ \item{base_size, base_family}{Base font size and family (passed to -\code{\link[ggplot2:ggtheme]{ggplot2::theme_bw()}}). It is possible to set \code{"bayesplot.base_size"} and +\code{\link[ggplot2:theme_bw]{ggplot2::theme_bw()}}). It is possible to set \code{"bayesplot.base_size"} and \code{"bayesplot.base_family"} via \code{\link[=options]{options()}} to change the defaults, which are \code{12} and \code{"serif"}, respectively.} } diff --git a/man/tidy-params.Rd b/man/tidy-params.Rd index b3cd4c5b..4def8d5d 100644 --- a/man/tidy-params.Rd +++ b/man/tidy-params.Rd @@ -21,7 +21,7 @@ subset of elements to select. For example, using would select parameters named \code{beta[1]}, \code{beta[2]}, and \code{beta[8]}. \code{param_range()} is only designed for the case that the indices are integers surrounded by brackets. If there are no brackets use -\link[tidyselect:language]{num_range()}.} +\link[tidyselect:select_helpers]{num_range()}.} \item{vars}{\code{NULL} or a character vector of parameter names to choose from. This is only needed for the atypical use case of calling the function as a @@ -56,11 +56,11 @@ everything-but selection (\code{vars(-alpha)}), ranged selection \strong{Examples} section, below. When using \code{pars} for tidy parameter selection, the \code{regex_pars} argument is -ignored because \strong{bayesplot} supports using \link[tidyselect:language]{tidyselect helper functions} (\code{starts_with()}, \code{contains()}, +ignored because \strong{bayesplot} supports using \link[tidyselect:select_helpers]{tidyselect helper functions} (\code{starts_with()}, \code{contains()}, \code{num_range()}, etc.) for the same purpose. \strong{bayesplot} also exports some additional helper functions to help with parameter selection: \itemize{ -\item \code{param_range()}: like \code{\link[tidyselect:starts_with]{num_range()}} but used +\item \code{param_range()}: like \code{\link[tidyselect:num_range]{num_range()}} but used when parameter indexes are in brackets (e.g. \code{beta[2]}). \item \code{param_glue()}: for more complicated parameter names with multiple indexes (including variable names) inside the brackets @@ -69,7 +69,7 @@ indexes (including variable names) inside the brackets These functions can be used inside of \code{vars()}, \code{dplyr::select()}, and similar functions, just like the -\link[tidyselect:language]{tidyselect helper functions}. +\link[tidyselect:select_helpers]{tidyselect helper functions}. } \section{Extra Advice}{