BayesHMM comes with many built-in visualization and text printout methods to carry out bayesian data analysis out of the box. All plot colors and printout text formats are based on a fully-customizable theme loaded as a global setting. The theme is simply a named list with two elements BayesHMM.theme and BayesHMM.print, which in turn are named lists following the structure described below. Run get_default_theme to see the default values.
BayesHMM.theme: settings for visualizations.
A character string with the color of the lines of the box corresponding to the observed sample. Applies to plot_ppredictive with features boxplot.
A character string with the color of the lines of the many boxes corresponding to the samples drawn from the posterior predictive density. Applies to plot_ppredictive with features boxplot.
A character string with the color of the cumulative density line for the observed sample. Applies to plot_ppredictive with features cumulative.
A character string with the color of the cumulative density lines for the many samples drawn from the posterior predictive density. Applies to plot_ppredictive with features cumulative.
A character string with the color of the density line for the observed sample. Applies to plot_ppredictive with features density.
A character string with the color of the density lines for the many samples drawn from the posterior predictive density. Applies to plot_ppredictive with features density.
A character string with the color of the border of the histogram bars. Applies to plot_ppredictive with features histogram.
A character string with the color of the area of the histogram bars. Applies to plot_ppredictive with features histogram.
A character string with the color of the vertical line related to the fun argument of the plot_ppredictive) function. The line is located at the value returned by fun applied to the actual sample. Applies to plot_ppredictive with features histogram.
A character string with the color of the border of the histogram bars. Applies to plot_ppredictive with features ks.
A character string with the color of the area of the histogram bars. Applies to plot_ppredictive with features ks.
A character string with the color of the point for the observed sample. Applies to plot_ppredictive with features scatterplot.
A character string with the color of the points for the many samples drawn from the posterior predictive density. Applies to plot_ppredictive with features scatterplot.
A character string with the color of the observation time series. Applies to plot_series and plot_state_probability.
A numeric value between zero and one with the transparency setting for the shaded features, where lower values lead to more transparent shading. Applies to plot_series and plot_state_probability.
A vector of character strings with the colors of each latent state. Applies to plot_series and plot_state_probability.
Note that the overall legend uses the colors densityY and densityYPred for the actual sample and the posterior predictive samples respectively.
BayesHMM.print: settings for text printouts.
A character to use to print text lines and boxes. It defaults to an underscore.
A character string to be used for indentation. It defaults to two spaces.
An integer with the width of the text lines and boxes. It defaults to 80 characters.
Other visualization functions: get_current_theme,
get_default_theme,
modify_theme_entry,
plot_ppredictive,
plot_series,
plot_state_probability