SimInf-package |
A Framework for Data-Driven Stochastic Disease Spread Simulations |
boxplot-method |
Box plot of number of individuals in each compartment |
C_code |
Extract the C code from a 'SimInf_model' object |
distance_matrix |
Create a distance matrix between nodes for spatial models |
events |
Extract the events from a 'SimInf_model' object |
events_SEIR |
Example data to initialize events for the 'SEIR' model |
events_SIR |
Example data to initialize events for the 'SIR' model |
events_SISe |
Example data to initialize events for the 'SISe' model |
events_SISe3 |
Example data to initialize events for the 'SISe3' model |
gdata |
Extract global data from a 'SimInf_model' object |
gdata<- |
Set a global data parameter for a 'SimInf_model' object |
indegree |
Determine in-degree for each node in a model |
ldata |
Extract local data from a node |
mparse |
Model parser to define new models to run in 'SimInf' |
Nn |
Extract number of nodes in a model |
nodes |
Example data with spatial distribution of nodes |
outdegree |
Determine out-degree for each node in a model |
package_skeleton |
Create a package skeleton from a 'SimInf_model' |
pairs-method |
Scatterplot of number of individuals in each compartment |
plot-method |
Display the distribution of scheduled events over time |
plot-method |
Display the outcome from a simulated trajectory |
prevalence |
Calculate prevalence from a model object with trajectory data |
punchcard<- |
Set a template for where to record result during a simualtion |
run |
Run the SimInf stochastic simulation algorithm |
run-method |
Run the SimInf stochastic simulation algorithm |
run_outer |
Run 'SimInf_model' on scaled parameters |
SEIR |
Create an SEIR model |
SEIR-class |
Definition of the 'SEIR' model |
select_matrix |
Extract the select matrix from a 'SimInf_model' object |
select_matrix<- |
Set the select matrix for a 'SimInf_model' object |
shift_matrix |
Extract the shift matrix from a 'SimInf_model' object |
shift_matrix<- |
Set the shift matrix for a 'SimInf_model' object |
show-method |
Brief summary of 'SimInf_events' |
show-method |
Brief summary of 'SimInf_model' |
SimInf |
A Framework for Data-Driven Stochastic Disease Spread Simulations |
SimInf_events |
Create a 'SimInf_events' object |
SimInf_events-class |
Class '"SimInf_events"' |
SimInf_model |
Create a 'SimInf_model' |
SimInf_model-class |
Class '"SimInf_model"' |
SIR |
Create an SIR model |
SIR-class |
Definition of the SIR model |
SISe |
Create a SISe model |
SISe-class |
Definition of the 'SISe' model |
SISe3 |
Create a 'SISe3' model |
SISe3-class |
Definition of the 'SISe3' model |
SISe3_sp |
Create a SISe3_sp model |
SISe3_sp-class |
Definition of the 'SISe3_sp' model |
SISe_sp |
Create a 'SISe_sp' model |
SISe_sp-class |
Definition of the 'SISe_sp' model |
summary-method |
Detailed summary of a 'SimInf_events' object |
summary-method |
Detailed summary of a 'SimInf_model' object |
trajectory |
Extract data from a simulated trajectory |
u0_SEIR |
Example data to initialize the 'SEIR' model |
u0_SIR |
Example data to initialize the 'SIR' model |
u0_SISe |
Example data to initialize the 'SISe' model |
u0_SISe3 |
Example data to initialize the 'SISe3' model |