diff --git a/doc/source/api/diffpy.srmise.applications.rst b/doc/source/api/diffpy.srmise.applications.rst
new file mode 100644
index 0000000..87413c9
--- /dev/null
+++ b/doc/source/api/diffpy.srmise.applications.rst
@@ -0,0 +1,28 @@
+:tocdepth: -1
+
+diffpy.srmise.applications package
+==================================
+
+.. automodule:: diffpy.srmise.applications
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+diffpy.srmise.applications.plot module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.applications.plot
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.applications.extract module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.applications.extract
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/api/diffpy.srmise.baselines.rst b/doc/source/api/diffpy.srmise.baselines.rst
new file mode 100644
index 0000000..5e9b791
--- /dev/null
+++ b/doc/source/api/diffpy.srmise.baselines.rst
@@ -0,0 +1,52 @@
+:tocdepth: -1
+
+diffpy.srmise.baselines package
+===============================
+
+.. automodule:: diffpy.srmise.baselines
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+diffpy.srmise.baselines.nanospherical module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.baselines.nanospherical
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.baselines.arbitrary module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.baselines.arbitrary
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.baselines.fromsequence module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.baselines.fromsequence
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.baselines.polynomial module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.baselines.polynomial
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.baselines.base module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.baselines.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/api/diffpy.srmise.example_package.rst b/doc/source/api/diffpy.srmise.example_package.rst
deleted file mode 100644
index 8c7f6ad..0000000
--- a/doc/source/api/diffpy.srmise.example_package.rst
+++ /dev/null
@@ -1,31 +0,0 @@
-.. _example_package documentation:
-
-|title|
-=======
-
-.. |title| replace:: diffpy.srmise.example_package package
-
-.. automodule:: diffpy.srmise.example_package
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-|foo|
------
-
-.. |foo| replace:: diffpy.srmise.example_package.foo module
-
-.. automodule::  diffpy.srmise.example_package.foo
-    :members:
-    :undoc-members:
-    :show-inheritance:
-
-|bar|
------
-
-.. |bar| replace:: diffpy.srmise.example_package.bar module
-
-.. automodule:: diffpy.srmise.example_package.foo
-    :members:
-    :undoc-members:
-    :show-inheritance:
diff --git a/doc/source/api/diffpy.srmise.modelevaluators.rst b/doc/source/api/diffpy.srmise.modelevaluators.rst
new file mode 100644
index 0000000..012c60a
--- /dev/null
+++ b/doc/source/api/diffpy.srmise.modelevaluators.rst
@@ -0,0 +1,36 @@
+:tocdepth: -1
+
+diffpy.srmise.modelevaluators package
+=====================================
+
+.. automodule:: diffpy.srmise.modelevaluators
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+diffpy.srmise.modelevaluators.aic module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.modelevaluators.aic
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.modelevaluators.aicc module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.modelevaluators.aicc
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.modelevaluators.base module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.modelevaluators.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/api/diffpy.srmise.peaks.rst b/doc/source/api/diffpy.srmise.peaks.rst
new file mode 100644
index 0000000..b88e831
--- /dev/null
+++ b/doc/source/api/diffpy.srmise.peaks.rst
@@ -0,0 +1,44 @@
+:tocdepth: -1
+
+diffpy.srmise.peaks package
+===========================
+
+.. automodule:: diffpy.srmise.peaks
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+Submodules
+----------
+
+diffpy.srmise.peaks.gaussianoverr module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.peaks.gaussianoverr
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.peaks.terminationripples module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.peaks.terminationripples
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.peaks.base module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.peaks.base
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.peaks.gaussian module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.peaks.gaussian
+    :members:
+    :undoc-members:
+    :show-inheritance:
diff --git a/doc/source/api/diffpy.srmise.rst b/doc/source/api/diffpy.srmise.rst
index 958efe0..98ea790 100644
--- a/doc/source/api/diffpy.srmise.rst
+++ b/doc/source/api/diffpy.srmise.rst
@@ -1,9 +1,7 @@
 :tocdepth: -1
 
-|title|
-=======
-
-.. |title| replace:: diffpy.srmise package
+diffpy.srmise package
+=====================
 
 .. automodule:: diffpy.srmise
     :members:
@@ -14,17 +12,100 @@ Subpackages
 -----------
 
 .. toctree::
-   diffpy.srmise.example_package
+    :titlesonly:
+
+    diffpy.srmise.peaks
+    diffpy.srmise.modelevaluators
+    diffpy.srmise.applications
+    diffpy.srmise.baselines
 
 Submodules
 ----------
 
-|module|
---------
+diffpy.srmise.multimodelselection module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.multimodelselection
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.srmiselog module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.srmiselog
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.modelparts module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.modelparts
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.peakstability module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.peakstability
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.basefunction module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.basefunction
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.pdfpeakextraction module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.pdfpeakextraction
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.modelcluster module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.modelcluster
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.dataclusters module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.dataclusters
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.srmiseerrors module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.srmiseerrors
+    :members:
+    :undoc-members:
+    :show-inheritance:
+
+diffpy.srmise.peakextraction module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+.. automodule:: diffpy.srmise.peakextraction
+    :members:
+    :undoc-members:
+    :show-inheritance:
 
-.. |module| replace:: diffpy.srmise.example_submodule module
+diffpy.srmise.pdfdataset module
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-.. automodule:: diffpy.srmise.example_submodule
+.. automodule:: diffpy.srmise.pdfdataset
     :members:
     :undoc-members:
     :show-inheritance: