om_code.getfitnesspenalty.getfitnesspenalty
om_code.getfitnesspenalty.getfitnesspenalty#
- getfitnesspenalty(self, ref, com, y='gr', abs=False, figs=True, nosamples=100, norm=False)[source]#
Calculates - as a measure of fitness - the area between typically two growth rate versus OD curves, normalized by the length along the OD-axis where they overlap.
- Parameters
- ref: list of strings
For only a single experiment, a list of two strings. The first string specifies the condition and the second specifies the strain to be used for the reference to which fitness is to be calculated. With multiple experiments, a list of three strings. The first string specifies the experiment, the second specifies the condition, and the third specifies the strain.
- com: list of strings
For only a single experiment, a list of two strings. The first string specifies the condition and the second specifies the strain to be compared with the reference. With multiple experiments, a list of three strings. The first string specifies the experiment, the second specifies the condition, and the third specifies the strain.
- y: string, optional
The variable to be compared.
- figs: boolean, optional
If True, a plot of the area between the two growth rate versus OD curves is shown.
- nosamples: integer
The number bootstraps used to estimate the error.
- norm: boolean
If True, returns the mean and variance of the area under the reference strain for normalisation.
- Returns
- fp: float
The area between the two curves.
- err: float
An estimate of the error in the calculated error, found by bootstrapping.
- reffp: float, optional
The area beneath the reference strain.
- referr: float, optional
An estimate of the erroe in the calculated area for the reference strain.