run_shiny {shinySIR}

Solve equations

Description

This function solves an ODE model using 'deSolve' and returns the output as a data frame.

Usage

run_shiny(model = "SIR", neweqns = NULL, ics = NULL, tstart = 0,
  timestep = 1, tmax = 365, parm0 = NULL, parm_names = NULL,
  parm_min = NULL, parm_max = NULL, sigfigs = 4, showtable = TRUE,
  linesize = 1.2, textsize = 14, xlabel = "Time",
  ylabel = "Number of individuals", legend_title = "Compartment",
  slider_steps = NULL, values = NULL, ...)

Arguments

model

name of the model to be solved. Examples of built-in models are: "SIR", "SIR vaccination". Default is "SIR".

neweqns

function specifying the equations of the user-defined model. Only to be used if a model is required that is not built-in. Default is NULL.

ics

named numeric vector specifying the initial conditions i.e. the initial values of all model variables. Default is c(S = 9999, I = 1, R = 0) for the SIR model.

tstart

numerical value of form c(tmin, tmax) indicating the time to start simulations. Default value is 0.

timestep

numerical value indicating time step be used when solving equations. Default value is 1/365.

tmax

numerical value indicating maximum time point to be considered.

parm0

named numeric vector of starting parameter values. Names must correspond to those used in the model equations.

parm_names

character vector of parameter names to be displayed in shiny menu. Must be in the same order as 'parm0'.

parm_min

named numeric vector of minimum parameter values.

parm_max

named numeric vector of maximum parameter values.

sigfigs

number of significant figures to round parameter input vectors. Default is 4.

showtable

logical TRUE/FALSE. Should the table of transformed parameters be shown? Only applies to built-in models. Default is TRUE.

linesize

numeric value for line width in ggplot output. Default is 1.2.

textsize

numeric value for textsize in ggplot output. Default is 14.

xlabel

character string for x axis plotting label. Default is "Time".

ylabel

character string for y axis plotting label. Default is "Number of individuals".

legend_title

character string for legend title. Default is "Compartment".

slider_steps

numeric vector of step size to include between slider input values. Should be NULL or a vector with an entry for each parameter input. Default is NULL.

values

vector specifying manual color scale (if desired). Length must equal the number of model variables.

...

extra argument to be passed through to ggplot scale_colour_manual: use 'labels' to change the legend names.

Value

data frame of model solutions in long format.

Examples

run_shiny(model = "SIR")