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fix typos in doc
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R/bayesplot-colors.R

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#'
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#' @return `color_scheme_set()` has the side effect of setting the color scheme
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#' used for plotting. It also returns ([invisibly][base::invisible]) a list of
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#' the hexidecimal color values used in `scheme`.
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#' the hexadecimal color values used in `scheme`.
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#'
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#' `color_scheme_get()` returns a list of the hexadecimal color
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#' values (without changing the current scheme). If the `scheme` argument
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#' @section Custom color schemes: A **bayesplot** color scheme consists of six
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#' colors. To specify a custom color scheme simply pass a character vector
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#' containing either the names of six [colors][grDevices::colors] or six
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#' hexidecimal color values (or a mix of names and hex values). The colors
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#' hexadecimal color values (or a mix of names and hex values). The colors
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#' should be in order from lightest to darkest. See the end of the
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#' **Examples** section for a demonstration.
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#'
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}
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if (length(not_found)) {
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abort(paste(
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"Each color must specified as either a hexidecimal color value ",
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"Each color must specified as either a hexadecimal color value ",
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"(e.g. '#C79999') or the name of a color (e.g. 'blue'). ",
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"The following provided colors were not found:",
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paste(unlist(not_found), collapse = ", ")

R/mcmc-combo.R

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#' `widths = c(2, 1)` will allocate more space for the first column by a
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#' factor of 2 (as would `widths = c(.3, .15)`, etc.). The default,
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#' `NULL`, allocates the same horizontal space for each column.
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#' @param gg_theme Unlike most of the other **bayesplot**functions,
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#' @param gg_theme Unlike most of the other **bayesplot** functions,
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#' `mcmc_combo` returns a gtable object rather than a ggplot object, and
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#' so theme objects can't be added directly to the returned plot object. The
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#' `gg_theme` argument helps get around this problem by accepting a
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#' **ggplot2** [theme][ggplot2::theme] object that is added to each of the
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#' plots *before* combining them into the gtable object that is returned.
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#' This can be a theme object created by a call to [ggplot2::theme()] or
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#' one of the **bayesplot**convenience functions, e.g.
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#' one of the **bayesplot** convenience functions, e.g.
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#' [legend_none()] (see the **Examples** section, below).
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#'
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#' @return A gtable object (the result of calling

R/ppc-overview.R

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#' overlaid. The x-axis variable can be optionally specified by the user
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#' (e.g. to plot against against a predictor variable or over time).
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#' * [__Predictive errors__][PPC-errors]: Plots of predictive errors
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#' (`y - yrep`) computed from `y` and eachc of the simulated datasets (rows)
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#' (`y - yrep`) computed from `y` and each of the simulated datasets (rows)
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#' in `yrep`. For binomial models binned error plots are also available.
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#' * [__Scatterplots__][PPC-scatterplots]: Scatterplots (and similar
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#' visualizations) of the data `y` vs. individual simuluted datasets
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#' visualizations) of the data `y` vs. individual simulated datasets
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#' (rows) in `yrep`, or vs. the average value of the distributions of each
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#' data point (columns) in `yrep`.
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#' * [__Plots for discrete outcomes__][PPC-discrete]: PPC functions that can

man/MCMC-combos.Rd

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man/PPC-overview.Rd

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man/bayesplot-colors.Rd

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vignettes/visual-mcmc-diagnostics.Rmd

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For an explanation of these warnings see
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[Divergent transitions after warmup](https://mc-stan.org/misc/warnings.html#divergent-transitions-after-warmup).
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We'll have a look at diagnosing the source of the divergences first and then
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dive into some diagnostics that should be checked even if there are no warnigns
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dive into some diagnostics that should be checked even if there are no warnings
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from the sampler.
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<br>
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[_Plotting MCMC draws_](https://mc-stan.org/bayesplot/articles/plotting-mcmc-draws.html)
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vignette also take optional arguments that can be used to display important
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HMC/NUTS diagnostic information. We'll see examples of this in the next
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section on divergenent transitions.
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section on divergent transitions.
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### Divergent transitions
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`mcmc_rhat_hist` for visualizing $\hat{R}$ estimates.
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First we'll quickly fit one of the models above again, this time intentionally
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using too few MCMC iterations and allowing more dispered initial values.
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using too few MCMC iterations and allowing more dispersed initial values.
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This should lead to some high $\hat{R}$ values.
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```{r, results='hide'}

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