Plot the thermal tolerance landscape

Draws the thermal tolerance landscape from derive_tdt_ttl(): survival over constant temperature and elapsed exposure time. The result is a ggplot object, to be refined by the user with further ggplot2 layers, scales, labels and themes.

Usage

plot_ttl(
  x,
  type = c("surface", "curves"),
  facet = TRUE,
  Ta = NULL,
  survival = c(0.1, 0.5, 0.9),
  labels = TRUE,
  time_unit = NULL
)

Arguments

x: A list, the output of derive_tdt_ttl().
type: A character string, either "surface" (the default) for the landscape as a map, or "curves" for survival curves at a few temperatures.
facet: A single logical value or the character string "all". TRUE (the default) gives a panel per setting of newdata, cut down to quartile values when there are many; "all" a panel for every setting; FALSE no panels.
Ta: An optional numeric vector of the temperatures to draw for type = "curves", each replaced by the nearest temperature of the landscape's grid. NULL (the default) takes the grid temperatures nearest its minimum, quartiles and maximum.
survival: A numeric vector of survival levels between 0 and 1, at which to draw the contour lines for type = "surface".
labels: A single logical value, whether to label each contour line of type = "surface" with its survival level.
time_unit: An optional character string giving the time unit for the axis label, e.g. "min". The fit does not record the unit of its times, so none is shown unless given.

Value

A ggplot object.

Details

With type = "surface" the whole landscape is drawn as a map, elapsed time across and temperature up, coloured by the posterior median survival from red (most have failed) through pale yellow (a survival of one half) to blue (most survive), with contour lines at the survival levels in survival, each labelled with its level. The credible interval is not shown on it. With type = "curves" survival is drawn against elapsed time at a few temperatures, each as the posterior median with its credible interval.

Elapsed time is on a log scale, unless the times include zero. The panels follow the same rule as in plot_tdt(), except that the map needs a panel for each setting of newdata, so facet = FALSE is refused for it when there are several.

Examples

if (FALSE) { # \dontrun{
# a model fitted to a small ramping trial: 20 individuals warmed from 20 to 35
# degrees over 60 minutes and checked every 10, in two trials (see fit_hazard())
path   <- data.frame(path_id = "A", time = c(0, 60), temp = c(20, 35))
checks <- data.frame(path_id = "A", time = seq(0, 60, by = 10))
ind    <- data.frame(id = 1:20, path_id = "A", event = 1, mass = runif(20, 8, 12),
                     trial = rep(c("a", "b"), each = 10),
                     t_upper = sample(seq(10, 60, 10), 20, replace = TRUE))
long   <- build_hazard_data(ind, path, "interval", covariates = c("mass", "trial"),
                            checks = checks)
fit    <- fit_hazard(long, "exp", dpar_formulas = list(loga = ~ 1 + mass))

tol <- derive_tdt_ttl(fit, newdata = data.frame(mass = c(8, 12)), t_ref = 60)
plot_ttl(tol, time_unit = "min")
plot_ttl(tol, type = "curves", Ta = c(22, 25, 28), time_unit = "min")
} # }