Package Bio :: Package phenotype :: Module pm_fitting
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Module pm_fitting

source code

Growth curves fitting and parameters extraction for phenotype data.

This module provides functions to perform sigmoid functions fitting to Phenotype Microarray data. This module depends on scipy curve_fit function. If not available, a warning is raised.

Functions: logistic Logistic growth model. gompertz Gompertz growth model. richards Richards growth model. guess_plateau Guess the plateau point to improve sigmoid fitting. guess_lag Guess the lag point to improve sigmoid fitting. fit Sigmoid functions fit. get_area Calculate the area under the PM curve.

Functions [hide private]
 
logistic(x, A, u, d, v, y0)
Logistic growth model.
source code
 
gompertz(x, A, u, d, v, y0)
Gompertz growth model.
source code
 
richards(x, A, u, d, v, y0)
Richards growth model (equivalent to Stannard).
source code
 
guess_lag(x, y)
Given two axes returns a guess of the lag point.
source code
 
guess_plateau(x, y)
Given two axes returns a guess of the plateau point.
source code
 
fit(function, x, y)
Fit the provided function to the x and y values.
source code
 
get_area(y, x)
Get the area under the curve.
source code
Function Details [hide private]

logistic(x, A, u, d, v, y0)

source code 

Logistic growth model.

Proposed in Zwietering et al., 1990 (PMID: 16348228)

gompertz(x, A, u, d, v, y0)

source code 

Gompertz growth model.

Proposed in Zwietering et al., 1990 (PMID: 16348228)

richards(x, A, u, d, v, y0)

source code 

Richards growth model (equivalent to Stannard).

Proposed in Zwietering et al., 1990 (PMID: 16348228)

guess_lag(x, y)

source code 

Given two axes returns a guess of the lag point.

The lag point is defined as the x point where the difference in y with the next point is higher then the mean differences between the points plus one standard deviation. If such point is not found or x and y have different lengths the function returns zero.

guess_plateau(x, y)

source code 

Given two axes returns a guess of the plateau point.

The plateau point is defined as the x point where the y point is near one standard deviation of the differences between the y points to the maximum y value. If such point is not found or x and y have different lengths the function returns zero.

fit(function, x, y)

source code 

Fit the provided function to the x and y values.

The function parameters and the parameters covariance.