sora.stats
The Parameters Class
- class sora.stats.Parameters[source]
Creates a dictionary of Parameter objects. The structure of this class heavely borrows its structure from parameters.py (lmfit)
The dictionary contains all the parameters necessary to perform the fit of a model/objective function.
- Parameters
dict (dict) – A dictionary of Parameter objects.
- _addpar(name, parameter)[source]
Private method to add the Parameter object to the Parameters dictionary.
- Parameters
name (string) – A name or label to describe the parameter
parameter (Parameter object) – Parameter object containing the parameter values
- Raises
ValueError – Error if passed object is not a valid Parameter object.
- add(name, value=None, minval=-inf, maxval=inf, free=True, std=None, initial_value=None)[source]
Include a Parameter values collection into the Parameters dictionary.
- Parameters
name (str) – A name or label to describe the parameter
value (float, optional) – When first created it contains the initial estimate of the parameter. In a result object it contains the best fit value, by default None.
minval (float, optional) – The lower bound used in the parameter variation, by default -inf
maxval (float, optional) – The upper bound used in the parameter variation, by default inf
free (bool, optional) – Defines if the parameter is allowed to vary, by default True
std (float, array) – In the result object it contains the computed uncertainty.
initial_value (float) – In the result object it contains the estimate before the fit.
- Returns
object – A Parameters object containing the collection of parameters.
- Return type
Parameters
- get_bounds(transposed=False)[source]
Method to get the bounds recorded in the Parameters object.
- Parameters
transposed (bool, optional) – Returns the bounds in a transposed array, by default False.
- Returns
array – Tuple array containing the bounds values.
- Return type
tuple
- get_names()[source]
Method to get the names of each parameter in the object.
- Returns
list – List of parameters names.
- Return type
str, list
- get_uncertainties()[source]
Method to get the uncertainties stored in the Parameters object.
- Returns
list – List of parameters uncertainties.
- Return type
float, list
- get_values()[source]
Method to get the values stored in the Parameters object.
- Returns
list – List of parameters values.
- Return type
float
- get_varys()[source]
Method to get the FREE values stored in the Parameters object.
- Returns
list – List of FREE parameters values.
- Return type
tuple
OptimizeResult Class
- class sora.stats.OptimizeResult(**kwargs)[source]
An object that contains the results obtained by the fitting procedure
- params
The best-fit parameters computed from the fit.
- Type
Parameters object
- method
Method used to compute the best fit solution.
- Type
str
- var_names
Ordered list of variable parameter names used in optimization, and useful for understanding the values in
initial_values
andcovar
.- Type
list
- covar
Scaled covariance matrix from minimization, with rows and columns corresponding to
var_names
. The covariance matrix is obtained from the approximation of the inverse of the Hessian matrix. This covariance matrix is scaled by the reduced chisqr.- Type
numpy.ndarray
- initial_values
Dictionary of initial values for varying parameters.
- Type
numpy.ndarray
- std
Array containing estimated N-sigma uncertainties, otherwise inf. Corresponding to
var_names
. In the least_squares case the formal numeric uncertainties are then derived from the covariance matrix. When uncertainties are unavailable Bootstraping can be used to derive the uncertainties. In this case confidence intervals (CI) limited by the provided sigma (z-score), e.g., 1-sigma CI will return the [0.16,0.84] quantiles as the low and high confidence intervals value.- Type
numpy.ndarray
- bootstrap
If not None, an array containing the bootstraped solutions for each variable (col), by defalut None.
- Type
None, numpy.ndarray
- success
True if optimization algorithm converged.
- Type
str
- nvars
Number of free variables used in fit.
- Type
int
- ndata
Number of data points.
- Type
int
- dof
Degrees of freedom in fit (ndata - nvars).
- Type
int
- residual
Residual array of the objective function when using the parameters best-fit solution.
- Type
numpy.ndarray
- chisqr
A weighted sum of squared deviations. If the objective function does not provide weighed residuals then it only expresses the sum of squared deviations.
- Type
float
- scipy
When scipy module is used the scipy.OptimizeResult object is also returned.
- Type
scipy.OptimizeResult object
- emcee
Describe
- Type
describe
- Returns
object – A OptimizeResult object containing the collection of the results obtained by the fit.
- Return type
OptimizeResult