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Plot full fits — plot.mcpfit • mcp

Plot prior or posterior model draws on top of data. Use plot_pars to plot individual parameter estimates.

# S3 method for mcpfit
plot(
  x,
  facet_by = NULL,
  lines = 25,
  geom_data = "point",
  cp_dens = TRUE,
  q_fit = FALSE,
  q_predict = FALSE,
  rate = TRUE,
  prior = FALSE,
  which_y = "ct",
  arma = TRUE,
  nsamples = 2000,
  scale = "response",
  ...
)

An mcpfit object

String. Name of a varying group.

Positive integer or FALSE. Number of lines (posterior draws). FALSE or lines = 0 plots no lines. Note that lines always plot fitted values - not predicted. For prediction intervals, see the q_predict argument.

String. One of "point" (default), "line" (good for time-series), or FALSE (don not plot).

TRUE/FALSE. Plot posterior densities of the change point(s)? Currently does not respect facet_by. This will be added in the future.

Whether to plot quantiles of the posterior (fitted value).

• TRUE: Add 2.5% and 97.5% quantiles. Corresponds to q_fit = c(0.025, 0.975).

• FALSE (default): No quantiles

• A vector of quantiles. For example, quantiles = 0.5 plots the median and quantiles = c(0.2, 0.8) plots the 20% and 80% quantiles.

Same as q_fit, but for the prediction interval.

Boolean. For binomial models, plot on raw data (rate = FALSE) or response divided by number of trials (rate = TRUE). If FALSE, linear interpolation on trial number is used to infer trials at a particular x.

TRUE/FALSE. Plot using prior samples? Useful for mcp(..., sample = "both")

What to plot on the y-axis. One of

• "ct": The central tendency which is often the mean after applying the link function (default).

• "sigma": The variance

• "ar1", "ar2", etc. depending on which order of the autoregressive effects you want to plot.

Whether to include autoregressive effects.

• TRUE: Compute autoregressive residuals. Requires the response variable in newdata.

• FALSE: Disregard the autoregressive effects. For family = gaussian(), predict() just use sigma for residuals.

Integer or NULL. Number of samples to return/summarise. If there are varying effects, this is the number of samples from each varying group. NULL means "all". Ignored if both are FALSE. More samples trade speed for accuracy.

One of

• "response": return on the observed scale, i.e., after applying the inverse link function.

• "linear": return on the parameter scale (where the linear trends are modelled).

Currently ignored.

A ggplot2 object.

plot() uses fit$simulate() on posterior samples. These represent the (joint) posterior distribution.

# Typical usage. ex_fit is an mcpfit object.
plot(ex_fit)
# \donttest{
plot(ex_fit, prior = TRUE)  # The prior

plot(ex_fit, lines = 0, q_fit = TRUE)  # 95% HDI without lines
plot(ex_fit, q_predict = c(0.1, 0.9))  # 80% prediction interval
plot(ex_fit, which_y = "sigma", lines = 100)  # The variance parameter on y

# Show a panel for each varying effect
# plot(fit, facet_by = "my_column")

# Customize plots using regular ggplot2
library(ggplot2)
plot(ex_fit) + theme_bw(15) + ggtitle("Great plot!")
# }

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