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R/bayesplot-ggplot-themes.R

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#'
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#' The [theme_default()] function returns the default ggplot
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#' [theme][ggplot2::theme] used by the **bayesplot** plotting functions. See
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#' [bayesplot_theme_set()] for details on setting and updating the plotting theme.
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#' [bayesplot_theme_set()] for details on setting and updating the plotting
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#' theme.
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#'
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#' @export
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#' @param base_size,base_family Base font size and family (passed to
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#' [ggplot2::theme_bw()]). It is possible to set `"bayesplot.base_size"` and
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#' `"bayesplot.base_family"` via [options()] to change the defaults, w
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#' hich are `12` and `"serif"`, respectively.
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#' `"bayesplot.base_family"` via [options()] to change the defaults, which are
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#' `12` and `"serif"`, respectively.
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#' @return A ggplot [theme][ggplot2::theme] object.
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#'
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#' @seealso [bayesplot_theme_set()] to change the ggplot theme.

R/mcmc-diagnostics-nuts.R

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#' Diagnostic plots for the No-U-Turn-Sampler (NUTS)
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#'
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#' Diagnostic plots for the No-U-Turn-Sampler (NUTS), the default MCMC algorithm
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#' used by [Stan](https://mc-stan.org). See the **Plot Descriptions** section, below.
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#' used by [Stan](https://mc-stan.org). See the **Plot Descriptions** section,
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#' below.
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#'
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#' @name MCMC-nuts
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#' @aliases NUTS
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#' \item{`mcmc_nuts_divergence()`}{
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#' Two plots:
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#' * Violin plots of `lp__|divergent__=1` and `lp__|divergent__=0`.
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#' * Violin plots of `accept_stat__|divergent__=1` and `accept_stat__|divergent__=0`.
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#' * Violin plots of `accept_stat__|divergent__=1` and
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#' `accept_stat__|divergent__=0`.
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#' }
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#'
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#' \item{`mcmc_nuts_stepsize()`}{
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#' * [mcmc_trace()]: show divergences as tick marks below the
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#' trace plot.
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#' * [mcmc_parcoord()]: change the color/size/transparency of lines
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#' correspondending to divergences.
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#' corresponding to divergences.
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#' * [mcmc_scatter()]: change the color/size/shape of points
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#' corresponding to divergences.
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#' * [mcmc_pairs()]: change the color/size/shape of points

man/MCMC-nuts.Rd

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man/theme_default.Rd

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