Dose Response Curve Fitting (thunor.curve_fit
)¶

exception
thunor.curve_fit.
AAFitWarning
¶

exception
thunor.curve_fit.
AUCFitWarning
¶

exception
thunor.curve_fit.
DrugCombosNotImplementedError
¶ This function does not support drug combinations yet

class
thunor.curve_fit.
HillCurve
(popt)¶ Base class defining Hill/loglogistic curve functionality

null_response_fn
(axis=None, dtype=None, out=None, keepdims=<no value>)¶ Compute the arithmetic mean along the specified axis.
Returns the average of the array elements. The average is taken over the flattened array by default, otherwise over the specified axis. float64 intermediate and return values are used for integer inputs.
Parameters:  a (array_like) – Array containing numbers whose mean is desired. If a is not an array, a conversion is attempted.
 axis (None or int or tuple of ints, optional) –
Axis or axes along which the means are computed. The default is to compute the mean of the flattened array.
New in version 1.7.0.
If this is a tuple of ints, a mean is performed over multiple axes, instead of a single axis or all the axes as before.
 dtype (datatype, optional) – Type to use in computing the mean. For integer inputs, the default is float64; for floating point inputs, it is the same as the input dtype.
 out (ndarray, optional) – Alternate output array in which to place the result. The default
is
None
; if provided, it must have the same shape as the expected output, but the type will be cast if necessary. See doc.ufuncs for details.  keepdims (bool, optional) –
If this is set to True, the axes which are reduced are left in the result as dimensions with size one. With this option, the result will broadcast correctly against the input array.
If the default value is passed, then keepdims will not be passed through to the mean method of subclasses of ndarray, however any nondefault value will be. If the subclass’ method does not implement keepdims any exceptions will be raised.
Returns: m – If out=None, returns a new array containing the mean values, otherwise a reference to the output array is returned.
Return type: ndarray, see dtype parameter above
See also
average()
 Weighted average
std()
,var()
,nanmean()
,nanstd()
,nanvar()
Notes
The arithmetic mean is the sum of the elements along the axis divided by the number of elements.
Note that for floatingpoint input, the mean is computed using the same precision the input has. Depending on the input data, this can cause the results to be inaccurate, especially for float32 (see example below). Specifying a higherprecision accumulator using the dtype keyword can alleviate this issue.
By default, float16 results are computed using float32 intermediates for extra precision.
Examples
>>> a = np.array([[1, 2], [3, 4]]) >>> np.mean(a) 2.5 >>> np.mean(a, axis=0) array([ 2., 3.]) >>> np.mean(a, axis=1) array([ 1.5, 3.5])
In single precision, mean can be inaccurate:
>>> a = np.zeros((2, 512*512), dtype=np.float32) >>> a[0, :] = 1.0 >>> a[1, :] = 0.1 >>> np.mean(a) 0.54999924
Computing the mean in float64 is more accurate:
>>> np.mean(a, dtype=np.float64) 0.55000000074505806


class
thunor.curve_fit.
HillCurveLL2
(popt)¶ 
classmethod
fit_fn
(x, b, e)¶ Two parameter loglogistic function (“Hill curve”)
Parameters:  x (np.ndarray) – Onedimensional array of “x” values
 b (float) – Hill slope
 e (float) – EC50 value
Returns: Array of “y” values using the supplied curve fit parameters on “x”
Return type: np.ndarray

classmethod
initial_guess
(x, y)¶ Heuristic function for initial fit values
Uses the approach followed by R’s drc library: https://cran.rproject.org/web/packages/drc/index.html
Parameters:  x (np.ndarray) – Array of “x” (dose) values
 y (np.ndarray) – Array of “y” (response) values
Returns: Fourvalued list corresponding to initial estimates of the parameters defined in the
ll4()
function.Return type: list

classmethod

class
thunor.curve_fit.
HillCurveLL3u
(popt)¶ Three parameter log logistic curve, for viability data

classmethod
fit_fn
(x, b, c, e)¶ Three parameter loglogistic function (“Hill curve”)
Parameters:  x (np.ndarray) – Onedimensional array of “x” values
 b (float) – Hill slope
 c (float) – Maximum response (lower plateau)
 e (float) – EC50 value
Returns: Array of “y” values using the supplied curve fit parameters on “x”
Return type: np.ndarray

classmethod
initial_guess
(x, y)¶ Heuristic function for initial fit values
Uses the approach followed by R’s drc library: https://cran.rproject.org/web/packages/drc/index.html
Parameters:  x (np.ndarray) – Array of “x” (dose) values
 y (np.ndarray) – Array of “y” (response) values
Returns: Fourvalued list corresponding to initial estimates of the parameters defined in the
ll4()
function.Return type: list

static
null_response_fn
(_)¶ Compute the arithmetic mean along the specified axis.
Returns the average of the array elements. The average is taken over the flattened array by default, otherwise over the specified axis. float64 intermediate and return values are used for integer inputs.
Parameters:  a (array_like) – Array containing numbers whose mean is desired. If a is not an array, a conversion is attempted.
 axis (None or int or tuple of ints, optional) –
Axis or axes along which the means are computed. The default is to compute the mean of the flattened array.
New in version 1.7.0.
If this is a tuple of ints, a mean is performed over multiple axes, instead of a single axis or all the axes as before.
 dtype (datatype, optional) – Type to use in computing the mean. For integer inputs, the default is float64; for floating point inputs, it is the same as the input dtype.
 out (ndarray, optional) – Alternate output array in which to place the result. The default
is
None
; if provided, it must have the same shape as the expected output, but the type will be cast if necessary. See doc.ufuncs for details.  keepdims (bool, optional) –
If this is set to True, the axes which are reduced are left in the result as dimensions with size one. With this option, the result will broadcast correctly against the input array.
If the default value is passed, then keepdims will not be passed through to the mean method of subclasses of ndarray, however any nondefault value will be. If the subclass’ method does not implement keepdims any exceptions will be raised.
Returns: m – If out=None, returns a new array containing the mean values, otherwise a reference to the output array is returned.
Return type: ndarray, see dtype parameter above
See also
average()
 Weighted average
std()
,var()
,nanmean()
,nanstd()
,nanvar()
Notes
The arithmetic mean is the sum of the elements along the axis divided by the number of elements.
Note that for floatingpoint input, the mean is computed using the same precision the input has. Depending on the input data, this can cause the results to be inaccurate, especially for float32 (see example below). Specifying a higherprecision accumulator using the dtype keyword can alleviate this issue.
By default, float16 results are computed using float32 intermediates for extra precision.
Examples
>>> a = np.array([[1, 2], [3, 4]]) >>> np.mean(a) 2.5 >>> np.mean(a, axis=0) array([ 2., 3.]) >>> np.mean(a, axis=1) array([ 1.5, 3.5])
In single precision, mean can be inaccurate:
>>> a = np.zeros((2, 512*512), dtype=np.float32) >>> a[0, :] = 1.0 >>> a[1, :] = 0.1 >>> np.mean(a) 0.54999924
Computing the mean in float64 is more accurate:
>>> np.mean(a, dtype=np.float64) 0.55000000074505806

classmethod

class
thunor.curve_fit.
HillCurveLL4
(popt)¶ 
aa
(min_conc, max_conc)¶ Find the activity area (area over the curve)
Parameters:  min_conc (float) – Minimum concentration to consider for fitting the curve
 max_conc (float) – Maximum concentration to consider for fitting the curve
Returns: Activity area value
Return type: float

auc
(min_conc)¶ Find the area under the curve
Parameters: min_conc (float) – Minimum concentration to consider for fitting the curve Returns: Area under the curve (AUC) value Return type: float

ec
(ec_num=50)¶ Find the effective concentration value (e.g. IC50)
Parameters: ec_num (int) – EC number between 0 and 100 (response level) Returns: Effective concentration value for requested response value Return type: float

classmethod
fit_fn
(x, b, c, d, e)¶ Four parameter loglogistic function (“Hill curve”)
Parameters:  x (np.ndarray) – Onedimensional array of “x” values
 b (float) – Hill slope
 c (float) – Maximum response (lower plateau)
 d (float) – Minimum response (upper plateau)
 e (float) – EC50 value
Returns: Array of “y” values using the supplied curve fit parameters on “x”
Return type: np.ndarray

ic
(ic_num=50)¶ Find the inhibitory concentration value (e.g. IC50)
Parameters: ic_num (int) – IC number between 0 and 100 (response level) Returns: Inhibitory concentration value for requested response value Return type: float

classmethod
initial_guess
(x, y)¶ Heuristic function for initial fit values
Uses the approach followed by R’s drc library: https://cran.rproject.org/web/packages/drc/index.html
Parameters:  x (np.ndarray) – Array of “x” (dose) values
 y (np.ndarray) – Array of “y” (response) values
Returns: Fourvalued list corresponding to initial estimates of the parameters defined in the
ll4()
function.Return type: list


class
thunor.curve_fit.
HillCurveNull
(popt)¶

exception
thunor.curve_fit.
ValueWarning
¶

thunor.curve_fit.
aa_obs
(responses, doses=None)¶ Activity Area (observed)
Parameters:  responses (np.array or pd.Series) – Response values, with dose values in the Index if a Series is supplied
 doses (np.array or None) – Dose values  only required if responses is not a pd.Series
Returns: Activity area (observed)
Return type: float

thunor.curve_fit.
fit_drc
(doses, responses, response_std_errs=None, fit_cls=<class 'thunor.curve_fit.HillCurveLL4'>, null_rejection_threshold=0.05, ctrl_dose_test=False)¶ Fit a dose response curve
Parameters:  doses (np.ndarray) – Array of dose values
 responses (np.ndarray) – Array of response values, e.g. viability, DIP rates
 response_std_errs (np.ndarray, optional) – Array of fit standard errors for the response values
 fit_cls (Class) – Class to use for fitting (default: 4 parameter log logistic “Hill” curve)
 null_rejection_threshold (float, optional) – pvalue for rejecting curve fit against no effect “flat” response model by Ftest (default: 0.05). Set to None to skip test.
 ctrl_dose_test (boolean) – If True, the minimum dose is assumed to represent control values (in DIP rate curves), and will reject fits where E0 is greater than a standard deviation higher than the mean of the control response values. Leave as False to skip the test.
Returns: A HillCurve object containing the fit parameters
Return type:

thunor.curve_fit.
fit_params
(ctrl_data, expt_data, fit_cls=<class 'thunor.curve_fit.HillCurveLL4'>, ctrl_dose_fn=<function <lambda>>)¶ Fit dose response curves to DIP rates or viability data
This method computes parameters including IC50, EC50, AUC, AA, Hill coefficient, and Emax. For a faster version, see
fit_params_minimal()
.Parameters:  ctrl_data (pd.DataFrame or None) – Control DIP rates from
dip_rates()
orctrl_dip_rates()
. Set to None to not use control data.  expt_data (pd.DataFrame) – Experiment (noncontrol) DIP rates from
dip_rates()
orexpt_dip_rates()
, or viability data fromviability()
 fit_cls (Class) – Class to use for curve fitting (default:
HillCurveLL4()
)  ctrl_dose_fn (function) – Function to use to set an effective “dose” (nonzero) for controls. Takes the list of experiment doses as an argument.
Returns: DataFrame containing DIP rate curve fits and parameters
Return type: pd.DataFrame
 ctrl_data (pd.DataFrame or None) – Control DIP rates from

thunor.curve_fit.
fit_params_from_base
(base_params, ctrl_resp_data=None, expt_resp_data=None, ctrl_dose_fn=<function <lambda>>, custom_ic_concentrations=frozenset(), custom_ec_concentrations=frozenset(), custom_e_values=frozenset(), custom_e_rel_values=frozenset(), include_aa=False, include_auc=False, include_hill=False, include_emax=False, include_einf=False, include_response_values=True)¶ Attach additional parameters to basic set of fit parameters

thunor.curve_fit.
fit_params_minimal
(ctrl_data, expt_data, fit_cls=<class 'thunor.curve_fit.HillCurveLL4'>, ctrl_dose_fn=<function <lambda>>)¶ Fit dose response curves to DIP or viability, and calculate statistics
This function only fits curves and stores basic fit parameters. Use
fit_params()
for more statistics and parameters.Parameters:  ctrl_data (pd.DataFrame or None) – Control DIP rates from
dip_rates()
orctrl_dip_rates()
. Set to None to not use control data.  expt_data (pd.DataFrame) – Experiment (noncontrol) DIP rates from
dip_rates()
orexpt_dip_rates()
 fit_cls (Class) – Class to use for curve fitting (default:
HillCurveLL4()
)  ctrl_dose_fn (function) – Function to use to set an effective “dose” (nonzero) for controls. Takes the list of experiment doses as an argument.
Returns: DataFrame containing DIP rate curve fits and parameters
Return type: pd.DataFrame
 ctrl_data (pd.DataFrame or None) – Control DIP rates from

thunor.curve_fit.
is_param_truncated
(df_params, param_name)¶ Checks if parameter values are truncated at boundaries of measured range
Parameters:  df_params (pd.DataFrame) – DataFrame of DIP curve fits with parameters from
fit_params()
 param_name (str) – Name of a parameter, e.g. ‘ic50’
Returns: Array of booleans showing whether each entry in the DataFrame is truncated
Return type: np.ndarray
 df_params (pd.DataFrame) – DataFrame of DIP curve fits with parameters from