[DOC] - Update API list

doc/api.rst

@@ -67,31 +67,15 @@ Functions to manipulate, examine, and analyze model objects.
    average_reconstructions
    fit_models_3d
 
-Component Objects
+Model Sub-Objects
 -----------------
 
 The model object combines multiple sub-objects that define and store different
-elements of the model definition, data, and results.
-
-Here, the main sub-objects are listed, some of which can also be used independently.
-
-Bands
-~~~~~
-
-An object for defining frequency band definitions.
-
-.. currentmodule:: specparam
-
-.. autosummary::
-   :toctree: generated/
-
-   Bands
+elements of the model definition, data, and results. Here, the main sub-objects are listed.
 
 Algorithm
 ~~~~~~~~~
 
-An object for defining fit algorithms.
-
 .. currentmodule:: specparam.algorithms.algorithm
 
 .. autosummary::
@@ -102,77 +86,116 @@ An object for defining fit algorithms.
 Modes
 ~~~~~
 
-An object for defining fit modes.
+.. currentmodule:: specparam.modes.modes
+
+.. autosummary::
+   :toctree: generated/
+
+   Modes
 
-.. currentmodule:: specparam.modes.mode
+Data
+~~~~
+
+.. currentmodule:: specparam.data.data
 
 .. autosummary::
    :toctree: generated/
 
-   Mode
+   Data
 
-Associated objects allow for defining mode parameters.
+Results
+~~~~~~~
 
-.. currentmodule:: specparam.modes.params
+.. currentmodule:: specparam.results.results
 
 .. autosummary::
    :toctree: generated/
 
-   ParamDefinition
+   Results
 
-Utility to check for available fit modes.
+Model Definitions
+-----------------
 
-.. currentmodule:: specparam.modes.definitions
+Spectral models are defined by the defining fit Modes. This section
+
+Mode
+~~~~
+
+The Mode object & related utilties, providing functionality for defining fit modes.
+
+.. currentmodule:: specparam.modes
 
 .. autosummary::
    :toctree: generated/
 
+   Mode
+   ParamDefinition
    check_modes
 
-Metrics
-~~~~~~~
-
-An object for defining metrics.
+Fit Functions (Aperiodic)
+~~~~~~~~~~~~~~~~~~~~~~~~~
 
-.. currentmodule:: specparam.metrics.metric
+.. currentmodule:: specparam.modes.funcs
 
 .. autosummary::
    :toctree: generated/
 
-   Metric
+   powerlaw_function
+   lorentzian_function
+   double_expo_function
 
-Utility to check for available metrics.
+Fit Functions (Peaks)
+~~~~~~~~~~~~~~~~~~~~~
 
-.. currentmodule:: specparam.metrics.definitions
+.. currentmodule:: specparam.modes.funcs
 
 .. autosummary::
    :toctree: generated/
 
-   check_metrics
+   gaussian_function
+   skewed_gaussian_function
+   cauchy_function
+   gamma_function
+   triangle_function
 
-Data
-~~~~
+Metrics
+-------
 
-An object for managing data to be modeled.
+The Metric object & related utilties, providing functionality for definining metrics to evaluate model fitting performance.
 
-.. currentmodule:: specparam.data.data
+Metric Object
+~~~~~~~~~~~~~
+
+.. currentmodule:: specparam.metrics
 
 .. autosummary::
    :toctree: generated/
 
-   Data
+   Metric
 
-Results
-~~~~~~~
+Metric Functions (Error)
+~~~~~~~~~~~~~~~~~~~~~~~~
 
-An object for managing model results.
+.. currentmodule:: specparam.metrics.error
 
-.. currentmodule:: specparam.results.results
+.. autosummary::
+   :toctree: generated/
+
+   compute_mean_abs_error
+   compute_mean_squared_error
+   compute_root_mean_squared_error
+   compute_median_abs_error
+
+Metric Functions (GoF)
+~~~~~~~~~~~~~~~~~~~~~~
+
+.. currentmodule:: specparam.metrics.gof
 
 .. autosummary::
    :toctree: generated/
 
-   Results
+   compute_r_squared
+   compute_adj_r_squared
 
 Data Objects
 ------------
@@ -240,6 +263,18 @@ The following functions operate on arrays of peak parameters, which may be usefu
     threshold_peaks
     sort_peaks
 
+Bands
+~~~~~
+
+An object for defining frequency band definitions.
+
+.. currentmodule:: specparam
+
+.. autosummary::
+   :toctree: generated/
+
+   Bands
+
 Measures
 --------
 

examples/customize/plot_custom_modes.py

@@ -86,7 +86,7 @@ def expo_only_function(xs, *params):
     xs : 1d array
         X-axis values.
     *params : float
-        Parameters that define the component fit.
+        Parameters that define the component fit: exponent.
 
     Returns
     -------
@@ -146,6 +146,7 @@ def expo_only_function(xs, *params):
     name='custom_expo_only',
     component='aperiodic',
     description='Fit an exponent only.',
+    formula=r'A(F) = 1/f^x',
     func=expo_only_function,
     jacobian=None,
     params=expo_only_params,
@@ -228,7 +229,7 @@ def rectangular_function(xs, *params):
     xs : 1d array
         X-axis values.
     *params : float
-        Parameters that define the component fit.
+        Parameters that define the component fit: ctr, hgt, wid.
 
     Returns
     -------
@@ -270,6 +271,7 @@ def rectangular_function(xs, *params):
     name='rectangular',
     component='periodic',
     description='Custom rectangular (boxcar) peak fit function.',
+    formula=None,
     func=rectangular_function,
     jacobian=None,
     params=rectangular_params,

examples/models/plot_model_component_relationships.py

@@ -22,7 +22,7 @@
 from specparam.convert.params import compute_peak_height
 
 # Import the default parameter conversions
-from specparam.modes.convert import DEFAULT_CONVERTERS
+from specparam.convert.definitions import DEFAULT_CONVERTERS
 
 # sphinx_gallery_start_ignore
 from specparam.plts.utils import check_ax

specparam/metrics/__init__.py

@@ -1 +1,3 @@
 """Metrics sub-module."""
+
+from .metric import Metric

specparam/metrics/definitions.py

@@ -84,4 +84,4 @@ def check_metrics():
         print('    {:8s} {:12s} : {:s}'.format(metric.category, metric.measure, metric.description))
 
 
-check_metric_definition = partial(check_selection, definition=Metric)
+check_metric_definition = partial(check_selection, options=METRICS, definition=Metric)

specparam/metrics/metrics.py

@@ -5,7 +5,7 @@
 import numpy as np
 
 from specparam.metrics.metric import Metric
-from specparam.metrics.definitions import METRICS, check_metric_definition
+from specparam.metrics.definitions import check_metric_definition
 from specparam.reports.strings import gen_metrics_str
 
 ###################################################################################################
@@ -63,7 +63,7 @@ def add_metric(self, metric):
         if isinstance(metric, dict):
             metric = Metric(**metric)
 
-        metric = check_metric_definition(metric, METRICS)
+        metric = check_metric_definition(metric)
 
         self.metrics.append(deepcopy(metric))
 

specparam/modes/__init__.py

@@ -1 +1,5 @@
 """Functionality related to definining fit modes."""
+
+from .mode import Mode
+from .params import ParamDefinition
+from .definitions import check_modes