Model: R6 class representing a mathematical model.
In junlingm/REpiSim: Mathematical Epidemiological Model Simulations in R
Model R Documentation
R6 class representing a mathematical model.
Description
R6 class representing a mathematical model.
R6 class representing a mathematical model.
Details
A mathematical model is described by a system of ODEs. The state variables
are called compartments, and the equations give the rate of change (i.e.,
the time derivatives of the states). An equation is specified by an
R formula, the parameters are automatically extracted. A model can then
be used to construct numerical or stochastic simulations, or be typeset
as latex equations.
The compartment name can coincide with a parameter name,
in which case the parameter is converted into a compartment. But the
name cannot conflict with another compartment or a substitution.
If the expression uses a compartment, then the parameter is considered
a compartment when simulating the model, i.e., it is returned as a column
in the data frame returned by the simulation.
The deleted compartment or substitution is converted to a
parameter. A parameter cannot be deleted. If the equation is changed
so that a parameter is not used by the model any more, then the paramter
is automatically removed.
The new name cannot conflict with another compartment,
substitution or paramter
Public fields
restricteda boolean variable indicating whether to restrict functions
allowed to be used in the ODE system. Default to FALSE
attached.functionsthe list of provided R functions to be used in
the model
Active bindings
compartmentsA read-only field that returns a character vector of compartment names
equationsA read-only field that returns a named list model equations
parametersA read-only field that returns a character vector of parameter names
substitutionsA read-only field that returns a named list of expressions
representationa read-only active field that returns the representation of the model
it returns a list that contains the equations substitutions. The compartmental model can
then be reconstructed from the representation.
ordera read-only active field that returns the order of the equations
and aliases that must appear to satisfy dependencies in calculation
missinga read-only field that returns the names of functions defined
neither in the global environment, nor in the attached.functions list.
Methods
Public methods
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Method new()
constructor
It constructs a Model object with compartments and substitutions.
Usage
Model$new(..., file = NULL, .restricted = FALSE)
Arguments
...Each extra parameter is either passed to the 'compartment' method
if it is a formula with the form 'name ~ value', or passed to the
'where' methods to define a substitution if it is a named expression.
fileif not NULL, a path or connection to a model file
to read the model from
.restricteda boolean variable indicating whether the ODE system
only has access to a limited set of functions. Default to TRUE
Examples
# An SIR model
SIR = Model$new(
S ~ -beta*S*I/N, # the dS/dt equation
I ~ beta*S*I/N - gamma*I, # the dI/dt equation
R ~ gamma*I, # the dR/dt equation
N = S + I + R # the total population N
)
print(SIR)
Method compartment()
define a compartment using a formula
Usage
Model$compartment(eq)
Arguments
eqa formula in the form of 'name ~ rate'. This defined a
compartment with a given name and rate of change.
Returns
The invisible object 'self' for chained operations
Examples
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
print(SIR)
Method where()
define parameters as substitutions
Usage
Model$where(..., pairs = NULL)
Arguments
...Each extra parameter must be named, which name is a parameter
and the value is the substitution.
pairsa named list, which is an alternative form to provide substitutions
Examples
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I)$
compartment(I ~ beta*S*I - gamma*I)$
compartment(R ~ gamma*I)$
where(pairs=list(beta=quote(b/N)))$
where(N = S + I + R)
print(SIR)
Method delete()
delete a compartment or a substitution
Usage
Model$delete(name)
Arguments
namea character specifying the name of the compartment
or the substitution to be deleted.
Returns
an invisible self to chain methods.
Examples
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
SIR$delete("N")
print(SIR)
Method rename()
rename a compartment, a substitution or a parameter
Usage
Model$rename(formula = NULL, from = NULL, to = NULL)
Arguments
formulathe @param from or @param to can be specified by a formula
in the form of 'from -> to' or 'to <- from'.
fromis the name of the compartment, substitution or paramter
to be changed.
tois the new name
Returns
an invisible self to chain methods
Examples
an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
SIR$rename(S->U)$rename(beta->b)
print(SIR)
Method format()
format the class for printing
Usage
Model$format()
Method clone()
The objects of this class are cloneable with this method.
Usage
Model$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Model$new`
## ------------------------------------------------
# An SIR model
SIR = Model$new(
S ~ -beta*S*I/N, # the dS/dt equation
I ~ beta*S*I/N - gamma*I, # the dI/dt equation
R ~ gamma*I, # the dR/dt equation
N = S + I + R # the total population N
)
print(SIR)
## ------------------------------------------------
## Method `Model$compartment`
## ------------------------------------------------
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
print(SIR)
## ------------------------------------------------
## Method `Model$where`
## ------------------------------------------------
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I)$
compartment(I ~ beta*S*I - gamma*I)$
compartment(R ~ gamma*I)$
where(pairs=list(beta=quote(b/N)))$
where(N = S + I + R)
print(SIR)
## ------------------------------------------------
## Method `Model$delete`
## ------------------------------------------------
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
SIR$delete("N")
print(SIR)
## ------------------------------------------------
## Method `Model$rename`
## ------------------------------------------------
an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
SIR$rename(S->U)$rename(beta->b)
print(SIR)
junlingm/REpiSim documentation built on June 15, 2025, 7:36 a.m.
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| Model | R Documentation |
R6 class representing a mathematical model.
Description
R6 class representing a mathematical model.
R6 class representing a mathematical model.
Details
A mathematical model is described by a system of ODEs. The state variables are called compartments, and the equations give the rate of change (i.e., the time derivatives of the states). An equation is specified by an R formula, the parameters are automatically extracted. A model can then be used to construct numerical or stochastic simulations, or be typeset as latex equations.
The compartment name can coincide with a parameter name, in which case the parameter is converted into a compartment. But the name cannot conflict with another compartment or a substitution.
If the expression uses a compartment, then the parameter is considered a compartment when simulating the model, i.e., it is returned as a column in the data frame returned by the simulation.
The deleted compartment or substitution is converted to a parameter. A parameter cannot be deleted. If the equation is changed so that a parameter is not used by the model any more, then the paramter is automatically removed.
The new name cannot conflict with another compartment, substitution or paramter
Public fields
restricteda boolean variable indicating whether to restrict functions allowed to be used in the ODE system. Default to FALSE
attached.functionsthe list of provided R functions to be used in the model
Active bindings
compartmentsA read-only field that returns a character vector of compartment names
equationsA read-only field that returns a named list model equations
parametersA read-only field that returns a character vector of parameter names
substitutionsA read-only field that returns a named list of expressions
representationa read-only active field that returns the representation of the model it returns a list that contains the equations substitutions. The compartmental model can then be reconstructed from the representation.
ordera read-only active field that returns the order of the equations and aliases that must appear to satisfy dependencies in calculation
missinga read-only field that returns the names of functions defined neither in the global environment, nor in the attached.functions list.
Methods
Public methods
Method new()
constructor
It constructs a Model object with compartments and substitutions.
Usage
Model$new(..., file = NULL, .restricted = FALSE)
Arguments
...Each extra parameter is either passed to the 'compartment' method if it is a formula with the form 'name ~ value', or passed to the 'where' methods to define a substitution if it is a named expression.
fileif not NULL, a path or connection to a model file to read the model from
.restricteda boolean variable indicating whether the ODE system only has access to a limited set of functions. Default to TRUE
Examples
# An SIR model SIR = Model$new( S ~ -beta*S*I/N, # the dS/dt equation I ~ beta*S*I/N - gamma*I, # the dI/dt equation R ~ gamma*I, # the dR/dt equation N = S + I + R # the total population N ) print(SIR)
Method compartment()
define a compartment using a formula
Usage
Model$compartment(eq)
Arguments
eqa formula in the form of 'name ~ rate'. This defined a compartment with a given name and rate of change.
Returns
The invisible object 'self' for chained operations
Examples
# an SIR model SIR = Model$new() SIR$compartment(S ~ -beta*S*I/N)$ compartment(I ~ beta*S*I/N - gamma*I)$ compartment(R ~ gamma*I)$ where(N = S + I + R) print(SIR)
Method where()
define parameters as substitutions
Usage
Model$where(..., pairs = NULL)
Arguments
...Each extra parameter must be named, which name is a parameter and the value is the substitution.
pairsa named list, which is an alternative form to provide substitutions
Examples
# an SIR model SIR = Model$new() SIR$compartment(S ~ -beta*S*I)$ compartment(I ~ beta*S*I - gamma*I)$ compartment(R ~ gamma*I)$ where(pairs=list(beta=quote(b/N)))$ where(N = S + I + R) print(SIR)
Method delete()
delete a compartment or a substitution
Usage
Model$delete(name)
Arguments
namea character specifying the name of the compartment or the substitution to be deleted.
Returns
an invisible self to chain methods.
Examples
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
SIR$delete("N")
print(SIR)
Method rename()
rename a compartment, a substitution or a parameter
Usage
Model$rename(formula = NULL, from = NULL, to = NULL)
Arguments
formulathe @param from or @param to can be specified by a formula in the form of 'from -> to' or 'to <- from'.
fromis the name of the compartment, substitution or paramter to be changed.
tois the new name
Returns
an invisible self to chain methods
Examples
an SIR model SIR = Model$new() SIR$compartment(S ~ -beta*S*I/N)$ compartment(I ~ beta*S*I/N - gamma*I)$ compartment(R ~ gamma*I)$ where(N = S + I + R) SIR$rename(S->U)$rename(beta->b) print(SIR)
Method format()
format the class for printing
Usage
Model$format()
Method clone()
The objects of this class are cloneable with this method.
Usage
Model$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
Examples
## ------------------------------------------------
## Method `Model$new`
## ------------------------------------------------
# An SIR model
SIR = Model$new(
S ~ -beta*S*I/N, # the dS/dt equation
I ~ beta*S*I/N - gamma*I, # the dI/dt equation
R ~ gamma*I, # the dR/dt equation
N = S + I + R # the total population N
)
print(SIR)
## ------------------------------------------------
## Method `Model$compartment`
## ------------------------------------------------
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
print(SIR)
## ------------------------------------------------
## Method `Model$where`
## ------------------------------------------------
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I)$
compartment(I ~ beta*S*I - gamma*I)$
compartment(R ~ gamma*I)$
where(pairs=list(beta=quote(b/N)))$
where(N = S + I + R)
print(SIR)
## ------------------------------------------------
## Method `Model$delete`
## ------------------------------------------------
# an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
SIR$delete("N")
print(SIR)
## ------------------------------------------------
## Method `Model$rename`
## ------------------------------------------------
an SIR model
SIR = Model$new()
SIR$compartment(S ~ -beta*S*I/N)$
compartment(I ~ beta*S*I/N - gamma*I)$
compartment(R ~ gamma*I)$
where(N = S + I + R)
SIR$rename(S->U)$rename(beta->b)
print(SIR)
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