Updated the README with additional information and sections. Added an…

… initial CHANGELOG.

CHANGELOG.md

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+# Change Log
+All notable changes to this project will be documented in this file.
+
+The format is based on [Keep a Changelog](http://keepachangelog.com/)
+and this project adheres to [Semantic Versioning](http://semver.org/).
+
+## [0.1.0] - 2023-05-23
+
+### Added
+- Initial development version of the package.
+
+## [Unreleased] - yyyy-mm-dd
+
+N/A
+
+### Added
+
+### Changed
+
+### Fixed

README.md

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 # pysb-pkpd
 
 PySB plugin package providing domain-specific macros and models for pharmacological PK/PD modeling.
+
+## Table of Contents
+
+ 1. [Install](#install)
+     1. [Dependencies](#dependencies)
+     2. [pip install](#pip-install)
+     3. [Manual install](#manual-install)
+ 2. [License](#license)
+ 3. [Change Log](#change-log)
+ 4. [Documentation and Usage](#documentation-and-usage)
+     1. [Quick Overview](#quick-overview)
+     2. [Example](#example)
+ 5. [Contact](#contact)
+ 6. [Citing](#citing)  
+
+------
+
+# Install
+
+| **! Note** |
+| :--- |
+|  psyb-pkpd is still in version zero development so new versions may not be backwards compatible. |
+
+**pysb-pkpd** installs as the `pysb.pkpd` Python (namespace) package. It is has been developed with Python 3.11.3 and PySB 1.15.0.
+
+### Dependencies
+
+Note that `pysb-pkpd` has the following core dependencies:
+   * [PySB](https://pysb.org/) - developed using PySB version 1.15.0
+
+
+### pip install
+
+You can install `pysb-pkpd` version 0.1.0 with `pip` sourced from the GitHub repo:
+
+##### with git installed:
+
+Fresh install:
+```
+pip install git+https://github.com/blakeaw/[email protected]
+```
+Or to upgrade from an older version:
+```
+pip install --upgrade git+https://github.com/blakeaw/[email protected]
+```
+##### without git installed:
+
+Fresh install:
+```
+pip install https://github.com/blakeaw/pysb-pkpd/archive/refs/tags/v0.1.0.zip
+```
+Or to upgrade from an older version:
+```
+pip install --upgrade https://github.com/blakeaw/pysb-pkpd/archive/refs/tags/v0.1.0.zip
+```
+### Manual install
+
+First, download the repository. Then from the `pysb-pkpd` folder/directory run
+```
+pip install .
+```
+
+------
+
+# License
+
+This project is licensed under the BSD 2-Clause License - see the [LICENSE](LICENSE) file for details
+
+------
+
+# Change Log
+
+See: [CHANGELOG](CHANGELOG.md)
+
+------
+
+# Documentation and Usage
+
+### Quick Overview
+
+`pysb-pkpd` defines a set of domain specific macros for PK/PD modeling using the PySB framework, as well as some pre-constructed versions of two and three-compartment PK and PK/PD models. As with PySB, `pysb-pkpd` is meant to be used to programatically construct models in Python. 
+
+### Example
+
+Building a two-compartment PK model with a sigmoidal Emax PD function:
+
+```python
+from pysb import Model, Monomer
+import pysb.pkpd as pkpd
+
+# Initialize the PySB model:
+Model()
+
+# Add a Monomer for the drug:
+Monomer("Drug")
+
+# Add the compartments for a two-compartment model:
+pkpd.macros.two_compartments(c1_name="CENTRAL",
+                             c1_size=2.0,
+                             c2_name="PERIPHERAL",
+                             c2_size=1.0)
+
+
+# Add a dose of the drug using an 
+# instantaneous 'bolus' dose in the central
+# compartment (initial amount of drug at time zero).
+#   Note that dose is an amount such as weight, mass, or moles,
+#     which will be converted automatically to an initial concentration
+#     as: 
+#         [Drug]_0 = dose / V_CENTRAL , 
+#     where V_CENTRAL is the size (i.e., volume) of the central compartment.
+pkpd.macros.dose_bolus(Drug, CENTRAL, dose=100.)
+
+# Add (1st order) distribution and re-distribution between the 
+# central and peripheral compartments:
+#    Note that klist is [k_distribute, k_redistribute]
+pkpd.macros.distribute(Drug, CENTRAL, PERIPHERAL, klist=[1.0, 1e-1])
+
+# Include linear elimination of Drug from the central compartment 
+# by processes like metabolism and renal excretion.
+pkpd.macros.eliminate(Drug, CENTRAL, kel=1e-2)
+
+# Add the sigmoidal Emax PD function for Drug in the
+# central compartment:
+pkpd.macros.sigmoidal_emax(Drug, CENTRAL, emax=1.,
+                                          ec50=10.,
+                                          n=1.7)
+
+```
+
+### List of macros
+
+The `pysb.pkpd.macros` module currently defines the following macros encoding PK, PD, and dosing functions:
+
+PK functions:
+
+  * `two_compartments` - adds two compartments to the model for a two-comaprtment PK model.
+  * `three_compartments` - adds three compartments to the model for a three-compartment PK model.
+  * `eliminate` - adds linear (1st-order) elimination of the specified drug/species from a compartment.
+  * `eliminate_mm` - add non-linear, Michaelis-Menten, elimination of the specified drug/species from a compartment.
+  * `clearance` - adds linear (1st-order) elimination of the specified drug/species from a compartment by systemic clearance.
+  * `distribute` - adds distribution/redistribution of the specified drug/species between two compartments.
+  * `transfer` - adds one-way transfer (distribution with no redistribution) of the specified drug/species from one compartment to another.
+
+PD functions:
+
+  * `emax` - Adds an Emax model expression for the specified drug/species in a given compartment.
+  * `sigmoidal_emax` - Adds a sigmoidal Emax model expression for the specified drug/species in a given compartment.
+
+Dosing functions:
+
+  * `dose_bolus` - adds an instantaneous bolus dose of the specified drug/species, defining the initial concentration at time zero.
+  * `dose_infusion` - adds a continous (zero-order) infusion of the specified drug/species. 
+
+### Pre-constructed models
+
+In addition to the macros module, `pysb-pkpd` includes some pre-constructed two-compartment and three-compartment models. 
+
+#### PK/PD models
+
+Two-compartment and three-compartment PK models with Emax PD function for the drug in the central compartment:
+```python
+from pysb.pkpd.pk_models import twocomp, threecomp
+```
+
+#### PK-only models
+
+Two-compartment and three-compartment PK models:
+```python
+from pysb.pkpd.models import twocomp_emax, threecomp_emax
+```
+
+
+------
+
+# Contact
+
+Please open a [GitHub Issue](https://github.com/blakeaw/pysb-pkpd/issues) to
+report any problems/bugs or make any comments, suggestions, or feature requests.
+
+------
+
+# Citing
+
+If this package is useful in your work, please cite this GitHub repo: https://github.com/blakeaw/pysb-pkpd