MA 5/7/16 
Metadata amended to reflect thesis by publication procedures. LM 07/02/20
Chapter 2 - permitted - creative commons license.
Chapter 3 - permitted - "Authors retain the right to: include the work in part or in full in a thesis provided it is not published for commercial gain" https://www.publish.csiro.au/journals/copyright.
Chapter 4 & 5 - permitted as unpublished.
Chapter 6 - version not specified, but isn't published version. According to Sherpa/Romeo http://sherpa.ac.uk/romeo/issn/1544-273X/ both pre and post versions are not permitted. Article removed and citation page inserted with published version DOI.
Chapter 7 - permitted - publisher is Elsevier - Elsevier has a policy of allowing published articles to remain in theses.  https://www.elsevier.com/about/policies/copyright/permissions (click on Can I include/use my article in my thesis/dissertation).