epipack
0.1.5
About
Tutorial
Introduction
Numeric Models
Symbolic Models
Network/Well-Mixed Simulations
Time-Varying Rates
Interactive Integrations
Visualizations
Reaction-Diffusion Systems
Temporal Networks
Dev Guide
State-Altering Tuples
Matrix-Based Models
Stochastic Simulations
Gillespie's SSA
Testing
Visualizations
Color Handling
API
Numeric Models
Symbolic Models
Stochastic Models
Temporal Networks
Process Conversions
Visualization
Interactive
Mock Samplable Set
Integrators
Networks
Colors
Numeric Matrix-Based Models
Symbolic Matrix-Based Models
Plot Tools
Distributions
epipack
»
Index
Index
A
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B
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C
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D
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E
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F
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G
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H
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I
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J
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L
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M
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N
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O
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P
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Q
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R
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S
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T
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U
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V
|
W
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X
|
Y
A
add_batch() (epipack.vis.App method)
add_fission_processes() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
add_fusion_processes() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
add_linear_events() (epipack.numeric_epi_models.EpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
add_linear_rates() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
add_quadratic_events() (epipack.numeric_epi_models.EpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
add_quadratic_rates() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
add_scaling_object() (epipack.vis.Scale method)
add_transition_processes() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
add_transmission_processes() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
affected_by_quadratic_process (epipack.numeric_matrix_epi_models.MatrixEpiModel attribute)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel attribute)
App (class in epipack.vis)
append_list() (epipack.vis.Curve method)
append_single_value() (epipack.vis.Curve method)
ax (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
B
batch (epipack.vis.Curve attribute)
birth_event_updates (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
birth_rate_functions (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
bottom (epipack.vis.Scale attribute)
bound_increase_factor (epipack.vis.Scale attribute)
brighter() (in module epipack.colors)
C
check_bounds() (epipack.vis.Scale method)
children (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
choice() (in module epipack.mock_samplable_set)
clear() (epipack.mock_samplable_set.MockSamplableSet method)
color (epipack.vis.Curve attribute)
colors (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
compartment_ids (epipack.numeric_epi_models.EpiModel attribute)
compartments (epipack.numeric_epi_models.EpiModel attribute)
(epipack.numeric_matrix_epi_models.MatrixEpiModel attribute)
(epipack.stochastic_epi_models.StochasticEpiModel attribute)
(epipack.stochastic_epi_models.StochasticSIModel attribute)
(epipack.stochastic_epi_models.StochasticSIRModel attribute)
(epipack.stochastic_epi_models.StochasticSISModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel attribute)
ConstantBirthRate (class in epipack.numeric_epi_models)
ConstantLinearRate (class in epipack.numeric_epi_models)
ConstantQuadraticRate (class in epipack.numeric_epi_models)
continuous_update (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
correct_for_dynamical_population_size (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
Curve (class in epipack.vis)
custom_choice() (in module epipack.numeric_epi_models)
D
darker() (in module epipack.colors)
directed (epipack.temporal_networks.TemporalNetwork attribute)
domain() (epipack.vis.Scale method)
dydt() (epipack.distributions.ExpChain method)
(epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel method)
DynamicBirthRate (class in epipack.numeric_epi_models)
DynamicLinearRate (class in epipack.numeric_epi_models)
DynamicQuadraticRate (class in epipack.numeric_epi_models)
E
edge_lists (epipack.temporal_networks.TemporalNetwork attribute)
EpiModel (class in epipack.numeric_epi_models)
epipack.colors
module
epipack.distributions
module
epipack.integrators
module
epipack.interactive
module
epipack.mock_samplable_set
module
epipack.networks
module
epipack.numeric_epi_models
module
epipack.numeric_matrix_epi_models
module
epipack.plottools
module
epipack.process_conversions
module
epipack.stochastic_epi_models
module
epipack.symbolic_epi_models
module
epipack.symbolic_matrix_epi_models
module
epipack.temporal_networks
module
epipack.vis
module
ExpChain (class in epipack.distributions)
extent() (epipack.vis.Scale method)
F
fig (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
find_fixed_points() (epipack.symbolic_epi_models.SymbolicMixin method)
fission_processes_to_events() (in module epipack.process_conversions)
fission_processes_to_rates() (in module epipack.process_conversions)
fit_chain_by_cdf() (in module epipack.distributions)
fit_chain_by_median_and_iqr() (in module epipack.distributions)
fixed_parameters (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
from_tacoma() (epipack.temporal_networks.TemporalNetwork class method)
fusion_processes_to_events() (in module epipack.process_conversions)
fusion_processes_to_rates() (in module epipack.process_conversions)
G
GeneralInteractiveWidget (class in epipack.interactive)
get_2D_lattice_links() (in module epipack.networks)
get_box_layout() (in module epipack.interactive)
get_cdf() (epipack.distributions.ExpChain method)
get_cdf_at_percentiles() (epipack.distributions.ExpChain method)
get_compartment() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.stochastic_epi_models.StochasticEpiModel method)
get_compartment_changes() (epipack.numeric_epi_models.EpiModel method)
(epipack.stochastic_epi_models.StochasticEpiModel method)
get_compartment_id() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.stochastic_epi_models.StochasticEpiModel method)
get_eigenvalues_at_disease_free_state() (epipack.symbolic_epi_models.SymbolicMixin method)
get_eigenvalues_at_fixed_point() (epipack.symbolic_epi_models.SymbolicMixin method)
get_event_rates() (epipack.numeric_epi_models.EpiModel method)
get_grid_layout() (in module epipack.networks)
get_jacobian_at_fixed_point() (epipack.symbolic_epi_models.SymbolicMixin method)
get_jacobian_leading_eigenvalue() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
get_mean() (epipack.distributions.ExpChain method)
get_median_and_iqr() (epipack.distributions.ExpChain method)
get_network_batch() (in module epipack.vis)
get_next_generation_matrix() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
get_next_generation_matrix_leading_eigenvalue() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
get_numerical_dydt() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicMixin method)
get_numerical_event_and_rate_functions() (epipack.numeric_epi_models.EpiModel method)
(epipack.symbolic_epi_models.SymbolicMixin method)
get_pdf() (epipack.distributions.ExpChain method)
get_random_layout() (in module epipack.networks)
get_reacting_node() (epipack.stochastic_epi_models.StochasticEpiModel method)
get_small_world_layout() (in module epipack.networks)
get_temporal_interpolation() (in module epipack.symbolic_epi_models)
get_time_leap() (epipack.stochastic_epi_models.StochasticEpiModel method)
get_time_leap_and_proposed_compartment_changes() (epipack.numeric_epi_models.EpiModel method)
get_total_event_rate() (epipack.stochastic_epi_models.StochasticEpiModel method)
get_transition_matrix() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
get_transmission_matrix() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
get_true_total_event_rate() (epipack.stochastic_epi_models.StochasticEpiModel method)
H
h2r() (in module epipack.colors)
I
init_gl() (epipack.vis.App method)
initial_population_size (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
integrate() (epipack.integrators.IntegrationMixin method)
integrate_and_return_by_index() (epipack.integrators.IntegrationMixin method)
integrate_and_return_by_index_until() (epipack.integrators.IntegrationMixin method)
integrate_dopri5() (in module epipack.integrators)
integrate_euler() (in module epipack.integrators)
integrate_ivp_until() (in module epipack.integrators)
integrate_SDE() (in module epipack.integrators)
integrate_until() (epipack.integrators.IntegrationMixin method)
IntegrationMixin (class in epipack.integrators)
InteractiveIntegrator (class in epipack.interactive)
items (epipack.mock_samplable_set.MockSamplableSet attribute)
J
jacobian() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicMixin method)
L
lbl (epipack.interactive.GeneralInteractiveWidget attribute)
left (epipack.vis.Scale attribute)
linear_event_updates (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
linear_rate_functions (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
linear_rates (epipack.numeric_matrix_epi_models.MatrixEpiModel attribute)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel attribute)
lines (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
LogRange (class in epipack.interactive)
loop_network (epipack.temporal_networks.TemporalNetwork attribute)
M
make_node_event() (epipack.stochastic_epi_models.StochasticEpiModel method)
make_random_node_event() (epipack.stochastic_epi_models.StochasticEpiModel method)
MatrixEpiModel (class in epipack.numeric_matrix_epi_models)
MatrixSEIRModel (class in epipack.numeric_matrix_epi_models)
MatrixSIModel (class in epipack.numeric_matrix_epi_models)
MatrixSIRModel (class in epipack.numeric_matrix_epi_models)
MatrixSIRSModel (class in epipack.numeric_matrix_epi_models)
MatrixSISModel (class in epipack.numeric_matrix_epi_models)
max_weight (epipack.mock_samplable_set.MockSamplableSet attribute)
mean_out_degree() (epipack.temporal_networks.TemporalNetwork method)
min_weight (epipack.mock_samplable_set.MockSamplableSet attribute)
MockSamplableSet (class in epipack.mock_samplable_set)
model (epipack.interactive.InteractiveIntegrator attribute)
(epipack.temporal_networks.TemporalNetworkSimulation attribute)
module
epipack.colors
epipack.distributions
epipack.integrators
epipack.interactive
epipack.mock_samplable_set
epipack.networks
epipack.numeric_epi_models
epipack.numeric_matrix_epi_models
epipack.plottools
epipack.process_conversions
epipack.stochastic_epi_models
epipack.symbolic_epi_models
epipack.symbolic_matrix_epi_models
epipack.temporal_networks
epipack.vis
N
N (epipack.temporal_networks.TemporalNetwork attribute)
N_comp (epipack.numeric_epi_models.EpiModel attribute)
(epipack.numeric_matrix_epi_models.MatrixEpiModel attribute)
(epipack.stochastic_epi_models.StochasticEpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel attribute)
node_status (epipack.stochastic_epi_models.StochasticEpiModel attribute)
O
ODEs() (epipack.symbolic_epi_models.SymbolicMixin method)
ODEs_jupyter() (epipack.symbolic_epi_models.SymbolicMixin method)
old_node_status (epipack.vis.SimulationStatus attribute)
on_draw() (epipack.vis.App method)
on_key_press() (epipack.vis.App method)
on_mouse_drag() (epipack.vis.App method)
on_mouse_scroll() (epipack.vis.App method)
on_resize() (epipack.vis.App method)
P
parameter_values (epipack.symbolic_epi_models.SymbolicEpiModel attribute)
paused (epipack.vis.SimulationStatus attribute)
plot() (in module epipack.plottools)
processes_to_events() (in module epipack.process_conversions)
processes_to_rates() (in module epipack.process_conversions)
Q
quadratic_event_updates (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
quadratic_rate_functions (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
quadratic_rates (epipack.numeric_matrix_epi_models.MatrixEpiModel attribute)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel attribute)
R
r2h() (in module epipack.colors)
Range (class in epipack.interactive)
rates_have_explicit_time_dependence (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
reactions_may_still_occur() (epipack.stochastic_epi_models.StochasticEpiModel method)
rescale() (epipack.vis.Curve method)
reset() (epipack.temporal_networks.TemporalNetworkSimulation method)
result_function (epipack.interactive.GeneralInteractiveWidget attribute)
return_compartments (epipack.interactive.InteractiveIntegrator attribute)
return_keys (epipack.interactive.GeneralInteractiveWidget attribute)
right (epipack.vis.Scale attribute)
S
sample() (epipack.mock_samplable_set.MockSamplableSet method)
sampling_dt (epipack.vis.SimulationStatus attribute)
Scale (class in epipack.vis)
scale (epipack.vis.Curve attribute)
scale() (epipack.vis.Scale method)
scalex() (epipack.vis.Scale method)
scaley() (epipack.vis.Scale method)
scaling_objects (epipack.vis.Scale attribute)
SEIRModel (class in epipack.numeric_epi_models)
set() (epipack.vis.Curve method)
set_conditional_link_transmission_processes() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_initial_conditions() (epipack.integrators.IntegrationMixin method)
set_linear_events() (epipack.numeric_epi_models.EpiModel method)
(epipack.symbolic_epi_models.SymbolicEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
set_linear_rates() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel method)
set_link_transmission_processes() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_network() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_node_status() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_node_statuses() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_node_transition_processes() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_parameter_values() (epipack.symbolic_epi_models.SymbolicMixin method)
set_processes() (epipack.numeric_epi_models.EpiModel method)
(epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
set_quadratic_events() (epipack.numeric_epi_models.EpiModel method)
(epipack.symbolic_epi_models.SymbolicEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
set_quadratic_rates() (epipack.numeric_matrix_epi_models.MatrixEpiModel method)
(epipack.symbolic_matrix_epi_models.SymbolicMatrixEpiModel method)
set_random_initial_conditions() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_simulation_has_ended() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_simulation_has_not_ended() (epipack.stochastic_epi_models.StochasticEpiModel method)
set_simulation_status() (epipack.vis.SimulationStatus method)
set_well_mixed() (epipack.stochastic_epi_models.StochasticEpiModel method)
SIModel (class in epipack.numeric_epi_models)
simulate() (epipack.numeric_epi_models.EpiModel method)
(epipack.stochastic_epi_models.StochasticEpiModel method)
(epipack.symbolic_epi_models.SymbolicODEModel method)
(epipack.temporal_networks.TemporalNetworkSimulation method)
simulation_ended (epipack.vis.SimulationStatus attribute)
simulation_has_ended() (epipack.stochastic_epi_models.StochasticEpiModel method)
SimulationStatus (class in epipack.vis)
SIRModel (class in epipack.numeric_epi_models)
SIRSModel (class in epipack.numeric_epi_models)
SISModel (class in epipack.numeric_epi_models)
StochasticEpiModel (class in epipack.stochastic_epi_models)
StochasticSIModel (class in epipack.stochastic_epi_models)
StochasticSIRModel (class in epipack.stochastic_epi_models)
StochasticSISModel (class in epipack.stochastic_epi_models)
strip_axis() (in module epipack.plottools)
SymbolicEpiModel (class in epipack.symbolic_epi_models)
SymbolicMatrixEpiModel (class in epipack.symbolic_matrix_epi_models)
SymbolicMatrixSIModel (class in epipack.symbolic_matrix_epi_models)
SymbolicMatrixSIRModel (class in epipack.symbolic_matrix_epi_models)
SymbolicMatrixSIRSModel (class in epipack.symbolic_matrix_epi_models)
SymbolicMatrixSISModel (class in epipack.symbolic_matrix_epi_models)
SymbolicMixin (class in epipack.symbolic_epi_models)
SymbolicODEModel (class in epipack.symbolic_epi_models)
SymbolicSIModel (class in epipack.symbolic_epi_models)
SymbolicSIRModel (class in epipack.symbolic_epi_models)
SymbolicSIRSModel (class in epipack.symbolic_epi_models)
SymbolicSISModel (class in epipack.symbolic_epi_models)
T
t (epipack.interactive.GeneralInteractiveWidget attribute)
(epipack.interactive.InteractiveIntegrator attribute)
(epipack.temporal_networks.TemporalNetwork attribute)
t0() (epipack.temporal_networks.TemporalNetwork method)
temporal_network (epipack.temporal_networks.TemporalNetworkSimulation attribute)
TemporalNetwork (class in epipack.temporal_networks)
TemporalNetworkSimulation (class in epipack.temporal_networks)
time_leap_ivp() (in module epipack.integrators)
time_leap_newton() (in module epipack.integrators)
tmax (epipack.temporal_networks.TemporalNetwork attribute)
tohex() (in module epipack.colors)
top (epipack.vis.Scale attribute)
torgb() (in module epipack.colors)
total_weight() (epipack.mock_samplable_set.MockSamplableSet method)
transition_processes_to_events() (in module epipack.process_conversions)
transition_processes_to_rates() (in module epipack.process_conversions)
transmission_processes_to_events() (in module epipack.process_conversions)
transmission_processes_to_rates() (in module epipack.process_conversions)
U
update() (epipack.vis.SimulationStatus method)
update_bounds() (epipack.vis.Curve method)
update_parameters() (epipack.interactive.GeneralInteractiveWidget method)
(epipack.interactive.InteractiveIntegrator method)
update_plot() (epipack.interactive.GeneralInteractiveWidget method)
(epipack.interactive.InteractiveIntegrator method)
update_xscale() (epipack.interactive.GeneralInteractiveWidget method)
(epipack.interactive.InteractiveIntegrator method)
update_yscale() (epipack.interactive.GeneralInteractiveWidget method)
(epipack.interactive.InteractiveIntegrator method)
use_ivp_solver (epipack.numeric_epi_models.EpiModel attribute)
V
vertex_list (epipack.vis.Curve attribute)
visualize() (in module epipack.vis)
visualize_reaction_diffusion() (in module epipack.vis)
W
weighted (epipack.temporal_networks.TemporalNetwork attribute)
weights (epipack.mock_samplable_set.MockSamplableSet attribute)
X
x0 (epipack.vis.Scale attribute)
x1 (epipack.vis.Scale attribute)
xmax (epipack.vis.Curve attribute)
xmin (epipack.vis.Curve attribute)
Y
y0 (epipack.numeric_epi_models.EpiModel attribute)
(epipack.symbolic_epi_models.SymbolicEpiModel attribute)
(epipack.vis.Scale attribute)
y1 (epipack.vis.Scale attribute)
ymax (epipack.vis.Curve attribute)
ymin (epipack.vis.Curve attribute)