Missing changes to the docker/README.md

I've added the missing changes to the README.md to reflect changes I've made in the Dockerfile.

docker/README.md

@@ -1,32 +1,59 @@
 # Running the code with Docker
 
 [Docker][] provides an alternative way to run the model without the need to
-manually setup or install any dependencies. For Linux or MacOs, from the root
+manually setup or install any dependencies. The Docker file contains the latest version of the model and can be used to run it independently of the repo. 
-directory of the project run the command:
 
+### Running on Linux or MacOS
 ```
-docker run --rm -it -v $(pwd):/var/model harrisonzhu5080/covid19model:latest $(id -u) $(id -g)
+docker run --rm -v $(pwd)/results:/var/model/results -v $(pwd)/figures:/var/model/figures harrisonzhu5080/covid19model:latest
 ```
 
-If your user is not in the docker group then you will need to run the above
+### Running on Windows using PowerShell
-command prefixed with `sudo`. The same applies to all following commands.
-
-In the above, the `-v $(pwd)/:/var/model` option makes the current directory
-accessible when the container is run. This means the code which is executed is
-that in the current directory and includes any changes made. The use of `$(id
--u)` and `$(id -g)` ensure that all model output files will be owned by the
-current user instead of root.
-
-If using Powershell on Windows, from the root directory of the project run the
-command:
 ```
-docker run --rm -it -v ${pwd}:/var/model harrisonzhu5080/covid19model:latest 0 0
+docker run --rm -v ${pwd}/results:/var/model/results -v ${pwd}/figures:/var/model/figures harrisonzhu5080/covid19model:latest
+```
+
+### Settings
+Two environment variables are supported for setting the model run parameters:
+* DEBUG=TRUE, performs a very fast debug run
+* FULL=TRUE, performs a full run of the model
+
+Those options can also be passed directly to base.r on the command line setting either `--full` or `--debug`. 
+
+When neither option is set a longer debug run is performed. For proper estimates always use `FULL=TRUE` or the `--full` flag. 
+
+The usual option of setting the user for Docker `--user $(id -u):$(id -g)` is also supported.
+
+## Running custom changes using Docker
+
+If you want to run your own changes in the Docker image above the whole work directory can be mounted as volume replacing, the contents in the Docker image itself. 
+
+### Linux or MacOS
+```
+docker run --rm -v $(pwd):/var/model harrisonzhu5080/covid19model:latest
+```
+
+Other files in the directory can also be run, using:
+
+```
+docker run --rm -v $(pwd):/var/model harrisonzhu5080/covid19model:latest Rscript <filename>
+```
+
+### Windows using PowerShell
+```
+docker run --rm -v ${pwd}:/var/model harrisonzhu5080/covid19model:latest
+```
+
+Other files in the directory can also be run, using:
+
+```
+docker run --rm -v ${pwd}:/var/model harrisonzhu5080/covid19model:latest Rscript <filename>
 ```
 
 [Docker]: https://www.docker.com/
 
 
-# Building the Docker image
+## Building the Docker image
 
 A Dockerfile is provided in the `docker` directory. To build an image containing
 all of the dependencies of the model run the following command from the root