mgrowthctrl
Get Started
Installation
Get Started
Tutorials
Simulating Consumer-Resource Dynamics
Advanced: Open-Loop Control of Microbiome Dynamics
Advanced: Closed-Loop Control of Microbiome Dynamics
Models
Consumer-Resource Model
Advanced: Diauxic Shift Model
Advanced: Base Model Class
Parameter Fitting
Least-Squares Fitting
MCMC Fitting
Control & Optimization
Introduction
Open-Loop Controller
Closed-Loop Controller
Advanced: Base Controller
Utilities
Data Loading
Visualization
Saving Data
mgrowthctrl
Index
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
X
|
Y
A
a (mgrowthctrl.models.crm.model.CRModelParams attribute)
ArrayBackend (class in mgrowthctrl.backends.array)
as_dict() (mgrowthctrl.models.crm.model.CRModelParams method)
B
b (mgrowthctrl.models.crm.model.CRModelParams attribute)
BaseController (class in mgrowthctrl.controllers.base)
BaseODEModel (class in mgrowthctrl.models.base)
C
ClosedLoopNeuralController (class in mgrowthctrl.controllers.closed_loop)
compute_loss() (mgrowthctrl.controllers.base.BaseController method)
compute_rhs() (mgrowthctrl.models.base.BaseODEModel method)
(mgrowthctrl.models.crm.model.CRModel method)
control_rhs() (mgrowthctrl.models.base.BaseODEModel method)
criterion (mgrowthctrl.controllers.base.BaseController attribute)
crm_fit_mcmc_from_df() (in module mgrowthctrl.models.crm.fit)
crm_fit_mechanistic() (in module mgrowthctrl.models.crm.fit)
CRModel (class in mgrowthctrl.models.crm.model)
CRModelParams (class in mgrowthctrl.models.crm.model)
D
D (mgrowthctrl.models.crm.model.CRModelParams attribute)
Dataloader (class in mgrowthctrl.utils.data)
DEFAULT_ROOT_URL (in module mgrowthctrl.utils.data)
DType (in module mgrowthctrl.models.crm.model)
E
end_time (mgrowthctrl.utils.data.Dataloader property)
evaluate() (mgrowthctrl.models.base.BaseODEModel method)
F
fit() (mgrowthctrl.controllers.base.BaseController method)
(mgrowthctrl.models.crm.model.CRModel method)
fit_least_squares() (mgrowthctrl.models.crm.model.CRModel method)
fit_mcmc() (mgrowthctrl.models.crm.model.CRModel method)
forward() (mgrowthctrl.controllers.base.BaseController method)
(mgrowthctrl.controllers.closed_loop.ClosedLoopNeuralController method)
(mgrowthctrl.controllers.open_loop.OpenLoopNeuralController method)
from_dict() (mgrowthctrl.models.crm.model.CRModel static method)
from_shapes() (mgrowthctrl.models.crm.model.CRModelParams static method)
from_single_species_data() (mgrowthctrl.models.crm.model.CRModel class method)
G
get_input_history() (mgrowthctrl.controllers.base.BaseController method)
(mgrowthctrl.controllers.closed_loop.ClosedLoopNeuralController method)
(mgrowthctrl.controllers.open_loop.OpenLoopNeuralController method)
get_params() (mgrowthctrl.models.crm.model.CRModel method)
K
k (mgrowthctrl.models.crm.model.CRModelParams attribute)
K_ij (mgrowthctrl.models.crm.model.CRModelParams attribute)
L
load_local_data() (mgrowthctrl.utils.data.Dataloader method)
load_remote_experiment() (mgrowthctrl.utils.data.Dataloader method)
LossFunction (in module mgrowthctrl.controllers.base)
M
mgrowthctrl.backends.array
module
mgrowthctrl.controllers.base
module
mgrowthctrl.controllers.closed_loop
module
mgrowthctrl.controllers.open_loop
module
mgrowthctrl.models.base
module
mgrowthctrl.models.crm.model
module
mgrowthctrl.utils.data
module
mgrowthctrl.utils.save
module
ModelNames (class in mgrowthctrl.models.base)
module
mgrowthctrl.backends.array
mgrowthctrl.controllers.base
mgrowthctrl.controllers.closed_loop
mgrowthctrl.controllers.open_loop
mgrowthctrl.models.base
mgrowthctrl.models.crm.model
mgrowthctrl.utils.data
mgrowthctrl.utils.save
N
n_resources (mgrowthctrl.controllers.base.BaseController attribute)
n_species (mgrowthctrl.controllers.base.BaseController attribute)
net (mgrowthctrl.controllers.closed_loop.ClosedLoopNeuralController attribute)
(mgrowthctrl.controllers.open_loop.OpenLoopNeuralController attribute)
NumpyBackend (class in mgrowthctrl.backends.array)
O
obs_dim (mgrowthctrl.controllers.closed_loop.ClosedLoopNeuralController attribute)
OpenLoopNeuralController (class in mgrowthctrl.controllers.open_loop)
P
ParamsDict (in module mgrowthctrl.models.crm.model)
plot_data_with_overlay() (in module mgrowthctrl.utils.plot)
plot_mcmc_error_evolution() (in module mgrowthctrl.utils.plot)
plot_parameter_distributions() (in module mgrowthctrl.utils.plot)
predict() (mgrowthctrl.models.base.BaseODEModel method)
predict_u() (mgrowthctrl.controllers.base.BaseController method)
R
r (mgrowthctrl.models.crm.model.CRModelParams attribute)
S
S (mgrowthctrl.models.base.ModelNames attribute)
S_err (mgrowthctrl.models.base.ModelNames attribute)
S_err_names (mgrowthctrl.utils.data.Dataloader property)
s_idx (mgrowthctrl.controllers.base.BaseController attribute)
S_in (mgrowthctrl.models.crm.model.CRModelParams attribute)
S_names (mgrowthctrl.utils.data.Dataloader property)
save_simulation_results() (in module mgrowthctrl.utils.save)
set_params() (mgrowthctrl.models.crm.model.CRModel method)
simulate() (mgrowthctrl.controllers.base.BaseController method)
(mgrowthctrl.models.crm.model.CRModel method)
solve() (mgrowthctrl.models.base.BaseODEModel method)
start_time (mgrowthctrl.utils.data.Dataloader property)
T
to_dict() (mgrowthctrl.models.crm.model.CRModel method)
TorchBackend (class in mgrowthctrl.backends.array)
X
X (mgrowthctrl.models.base.ModelNames attribute)
X_err (mgrowthctrl.models.base.ModelNames attribute)
X_err_names (mgrowthctrl.utils.data.Dataloader property)
x_idx (mgrowthctrl.controllers.base.BaseController attribute)
X_names (mgrowthctrl.utils.data.Dataloader property)
Y
y0 (mgrowthctrl.utils.data.Dataloader property)