Display change in predicted event rate with age — plot_event

Useful function for creating a good-quality line graph of changes in predicted event rate with age.

If you want more control over the style of the graph, use the compute_fitted_event_rate() function to directly retrieve the predicted data.

Useful function for creating a good-quality line graph of changes in the empirical mortality rate.

You don't need to fit with lifelihood() to use this function, only to retrieve a lifelihood data object with as_lifelihoodData()

If you want more control over the style of the graph, use the compute_observed_event_rate() function to retrieve data.

Convenient function used in plot_observed_event_rate() and plot_fitted_event_rate().

Usage

plot_fitted_event_rate(
  lifelihoodResults,
  interval_width,
  event = c("mortality", "maturity", "reproduction"),
  newdata = NULL,
  add_observed_event_rate = TRUE,
  min_sample_size = 1,
  max_time = NULL,
  groupby = NULL,
  use_facet = FALSE,
  se.fit = FALSE,
  xlab = "Time",
  ylab = "Event Rate",
  type = "points"
)

plot_observed_event_rate(
  lifelihoodData,
  interval_width,
  event = c("mortality", "maturity", "reproduction"),
  max_time = NULL,
  min_sample_size = 1,
  groupby = NULL,
  use_facet = FALSE,
  xlab = "Time",
  ylab = "Mortality Rate"
)

plot_event_rate(
  rate_df,
  max_time,
  type = c("points", "lines"),
  groupby,
  use_facet,
  xlab = "Time",
  ylab = "Event rate",
  fitted_data = FALSE,
  plot_ci = FALSE
)

Arguments

lifelihoodResults: Output of lifelihood().
interval_width: The interval width used to calculate the event rate.
event: Which event to compute? Must be one of "mortality", "maturity", "reproduction".
newdata: Optional data.frame providing covariate values for prediction. If NULL, the original model data are used.
add_observed_event_rate: Boolean to add the observed event rate to the graph (default=TRUE).
min_sample_size: The minimum number of individuals alive at the beggining of a time interval for computing the observed event rate.
max_time: The maximum time for calculating the event rate. If set to NULL, the time of the last observed death is used.
groupby: Factor(s) whosse levels over which event rate should be represented (default=NULL).
use_facet: Use facet_wrap to plot one panel per group (default=FALSE).
se.fit: Whether or not to plot standard errors. Requires to fit MCMC when fitting with lifelihood() with the MCMC argument.
xlab: Label for x-axis (default="Time").
ylab: Label for y-axis (default="Event rate").
type: The type of symbol to be used for the plot (either of "points" or 'lines").
lifelihoodData: lifelihoodData object created with as_lifelihoodData().
rate_df: Dataframe with event rate.
fitted_data: Boolean indicating if the data is fitted (default=FALSE).
plot_ci: Boolean indicating if confidence intervals should be plotted (default=FALSE). Requires CI_2.5% and CI_97.5% columns in rate_df.

Value

a ggplot2 plot

Details

This function requires ggplot2 to be installed.