Source code for phenotypic.schema._log_growth_model

"""Fitted parameters and bounds for the logistic growth model."""

from ._measurement_info import Entry
from ._tiers import DerivedMeasure




class LOG_GROWTH_MODEL(DerivedMeasure):
    """Fitted parameters and bounds of the logistic growth model.

    Output columns are **metric-qualified**: each header is
    ``LogGrowthModel_<metric>_<parameter>``, where ``<metric>`` records the
    measurement the model was fit on (``self.on`` with its category prefix
    stripped, e.g. ``Shape_Area`` → ``Area``). For example, fitting on
    ``Shape_Area`` emits ``LogGrowthModel_Area_r`` (intrinsic growth rate) and
    ``LogGrowthModel_Area_µmax`` (maximum specific growth rate). The labels
    below are the ``<parameter>`` segment; the ``<metric>`` infix is filled in
    at fit time.
    """



    @classmethod
    def category(cls) -> str:
        return "LogGrowthModel"




    @classmethod
    def header_scheme(cls) -> str:
        return "metric_qualified"


    R_FIT = Entry("r", "The intrinsic growth rate",
                  tier=1, derivation_type="parameterization", derives_from="SIZE")
    K_FIT = Entry("K", "The carrying capacity",
                  tier=1, derivation_type="parameterization", derives_from="SIZE")
    N0_FIT = Entry("N0", "The initial number of the colony size metric being fitted",
                   tier=1, derivation_type="parameterization", derives_from="SIZE")
    LAM = Entry(
        "lambda",
        "The regularization factor applied to the max specific growth rate "
        "and initial population size",
        derivation_type="diagnostic",
    )
    BETA = Entry(
        "beta",
        (
            "The penalty factor applied to relative difference of "
            "the carrying capacity from the largest measurement"
        ),
        derivation_type="diagnostic",
    )
    GROWTH_RATE = Entry("µmax", "The growth rate of the colony calculated as (K*r)/4",
                        tier=1, derivation_type="parameterization", derives_from="SIZE")
    K_MAX = Entry("Kmax", "The upper bound of the carrying capacity for model fitting",
                  derivation_type="diagnostic")