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Plot Vibrio Decay Rate as a Function of Environmental Suitability

Source: R/plot_vibrio_decay_rate.R
plot_vibrio_decay_rate.Rd

This function generates a plot that visualizes the suitability-dependent decay rate of V. cholerae survival based on climate-driven environmental suitability (\(\psi_{jt}\)). The figure compares five transformation types for survival time using the cumulative Beta distribution:

  • Linear: \(f(\psi_{jt}) = \text{pbeta}(\psi_{jt} \mid s_1 = 1, s_2 = 1)\)

  • Concave: \(f(\psi_{jt}) = \text{pbeta}(\psi_{jt} \mid s_1 = 1, s_2 = 5)\)

  • Convex: \(f(\psi_{jt}) = \text{pbeta}(\psi_{jt} \mid s_1 = 5, s_2 = 1)\)

  • Sigmoidal: \(f(\psi_{jt}) = \text{pbeta}(\psi_{jt} \mid s_1 = 5, s_2 = 5)\)

  • Arcsine: \(f(\psi_{jt}) = \text{pbeta}(\psi_{jt} \mid s_1 = 0.5, s_2 = 0.5)\)

Usage

plot_vibrio_decay_rate(PATHS, decay_days_short = 3, decay_days_long = 90)

Arguments

PATHS

A list containing path locations for saving output. Must include:

  • DOCS_FIGURES: File path to the directory for saving the plot

decay_days_short

Numeric. Minimum survival time (in days). Default is 3.

decay_days_long

Numeric. Maximum survival time (in days). Default is 90.

Value

Saves a PNG file to PATHS$DOCS_FIGURES. Invisibly returns the ggplot object.

Details

The primary y-axis shows survival time in days. The secondary y-axis shows the decay rate \(\delta_{jt} = 1 / \text{days}(\psi_{jt})\). Horizontal dashed lines indicate the minimum and maximum bounds on survival time. The output plot is saved as a PNG file in the directory specified by PATHS$DOCS_FIGURES.

Examples

if (FALSE) { # \dontrun{
PATHS <- get_paths()
plot_vibrio_decay_rate(PATHS)
plot_vibrio_decay_rate(PATHS, decay_days_short = 2, decay_days_long = 100)
} # }