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Plot PM_model objects

Source: R/plotPM_model.R
plot.PM_model.Rd

[Stable]

Plots a PM_model based on differential equations using network plots from tidygraph and ggraph packages.

Usage

# S3 method for PM_model
plot(x, marker = TRUE, line = TRUE, explicit, implicit, ...)

Arguments

x

The name of an PM_model object.

marker

Controls the characteristics of the compartments (nodes). It can be boolean or a list. TRUE will plot the compartments with default characteristics. FALSE will suppress compartment plotting. If a list, can control some marker characteristics, including overriding defaults. These include:

  • color Marker color (default: dodgerblue).

  • opacity Ranging between 0 (fully transparent) to 1 (fully opaque). Default is 0.5.

  • size Relative size of boxes, ranging from 0 to 1. Default is 0.25.

  • line A list of additional attributes governing the outline for filled shapes, most commonly color (default: black) and width (default: 0.5).



Example: marker = list(color = "red", opacity = 0.8, line = list(color = "black", width = 1))

line

Controls characteristics of arrows (edges). TRUE will plot default lines. FALSE will suppress lines. If a list, can control some line characteristics, including overriding defaults. These include:

  • color Line color (default: black)

  • width Thickness in points (default: 1).



Example: line = list(color = "red", width = 2)

explicit

A data frame or tibble containing two columns named from and to to add additional connecting arrows to the plot indicating transfer between compartments. For each row, the from column contains the compartment number of the arrow origin, and the to column contains the compartment number of the arrow destination. Use 0 to indicate a destination to the external sink. e.g., explicit = data.frame(from = 3, to = 0)

implicit

Similar to explicit, used to add dashed connecting arrows to the plot indicating implicit transfer between compartments. For each row, the from column contains the compartment number of the arrow origin, and the to column contains the compartment number of the arrow destination. Use 0 to indicate a destination to the external sink. e.g., implicit = data.frame(from = 2, to = 4)

...

Not used.

Value

Plots the object.

Details

This accepts a PM_model object and creates a network plot where nodes are compartments and edges are arrows connecting compartments.

See also

PM_model, ggraph::ggraph(), ggplot2::ggplot()

Other PMplots: plot.MMopt(), plot.PM_cov(), plot.PM_cycle(), plot.PM_data(), plot.PM_final(), plot.PM_op(), plot.PM_pta(), plot.PM_sim(), plot.PM_valid()

Author

Markus Hovd, Julian Otalvaro, Michael Neely

Examples

library(PmetricsData)
NPex$model$plot()