GIS4102 - GIS PROGRAMMING: Participation Assignment #2 ~ GIS for Monitoring Animal Diseases

GIS has been shown to be of benefit in the field of veterinary science. In her 2001 paper, "Geographical Information System (GIS) as a Tool in Surveillance and Monitoring of Animal Diseases", published in Acta Veterinaria Scandinavica, Madelaine Norstrøm overviewed the possibilities and potential uses of GIS with respect to animal diseases.

Along with a general description of GIS, Norstrøm noted that tables of information could be joined with geographical data utilizing a common identifier (ID). She mentioned that numbers are preferable for IDs to reduce the chance of misspellings with character variables. The easily understood format of a map can be used to report disease information (incidence, prevalence, mortality, and morbidity) at the farm, region or national level. Density maps can be used in movie format to show the spread of disease. Real time outbreak notification is possible as is updated information for farm personnel and reports for authorities and the media. This use would be especially beneficial during an emergency situation.

Western Fjord Cattle
Photo Credit:  Anna Rehnberg
http://sciencenordic.com/endangered-norwegian-livestock-hanging

Using GIS, the locations of the case farm and at-risk farms can be identified in the event of an infectious disease outbreak. Buffer zones can be created around these as well as other risk areas such as markets, roads, and slaughter houses. With this information, veterinary personnel can develop a plan of action. Norstrøm stressed the importance of performing a cluster analysis related to time and space to minimize misinterpretation of visual point patterns on maps. The integration of simulation models within a GIS utilizes risk factors for the spread of disease.

Norstrøm continued with an explanation of what data is available and where to obtain it. She mentioned that the goal is to have maps continuously displaying each disease's status. Norstrøm concluded with two specific examples of GIS use for specific swine and cattle diseases.

GIS4102 Participation Assignment #1: Ethics and Privacy Issues in the Use of GIS

The following is a summary of Ethics and Privacy Issues in the Use of GIS by Amy J. Blatt, Journal of Map and Geography Libraries, 8:80-84, 2012.

The increasing use of GIS across diverse disciplines includes ethics and privacy matters which Amy J. Blatt addresses in "Ethics and Privacy in the Use of GIS". Blatt focused on academic map and geography libraries' handling and distribution of geospatial datasets which are now being distributed to health care delivery and service providers outside the realm of medical research. Blatt stresses that map and geography librarians must be aware of privacy and ethics issues when individuals' personal health and cadastral data are used including in planning and medical geography. For instance, public health researchers can obtain patient records for research purposes. This information (names, addresses, phone, social security numbers, account numbers, images, etc.) is protected by HIPAA's privacy rules to prevent unauthorized use and must be protected while being transferred electronically.

Blatt also discussed planning. Cadastral datasets can include owner's name, address, assessed value, property boundaries, and more. At the time of the article's publication, there was little federal protection of this information. Local municipalities and jurisdictions allow individual, personal information to be made public as they see fit. (Identical information collected by the US Census Bureau may not be published.) Since there are no laws forbidding acquiring and cross-referencing parcel data and individual sales data, a market research firm could do this legally, although it would raise ethical issues.

Blatt suggests that map and geography libraries ensure that HIPAA regulations are followed when handling and distributing personal medical data; include comprehensive metadata with all datasets, and develop codes of conduct which address uses (ethical and unethical) of geospatial data. She concludes with stating that when no federal laws govern the use of geospatial data, individuals are responsible for determining whether their use of GIS (proposed or intended) would be viewed as unethical by those affected.

While searching for an article to summarize, the following article and website of interest were also discovered:

http://www.spatial.maine.edu/~onsrud/GISlaw.htm link to additional resources (hasn’t been updated for a few years)

http://www.geolawpc.com/faq.html law firm specializing in “spatial law”

GIS4102 Module 4: Python Fundamentals Part II

The focus of this week's exercise and assignment was continuing practice of and developing familiarity with Python scripting. The emphasis was on importing modules, troubleshooting code (many opportunities arise for this in my particular case), creating while loops and conditional statements, adding comments, and iterating variables within loops. The first portion of the assignment involved the import of a module and troubleshooting the code provided for a dice game with random number generation.

The script-creating portion of this assignment included developing a while loop to add 20 random integers between 0 and 10 to a list. From that list one number was eliminated and the number of times it had occurred was printed in a message. For random-generations in which the number did not occur, a different message was printed. The screenshots included here show an example of each message:

The Number 5 Eliminated from List
and Associated Message

The Number 5 Does Not Occur in List
with Associated Message

The error message returned at the second while loop I initially coded was a bit deceptive, notifying me that my variable was not in the list although it could be printed out. After trying to troubleshoot it in one manner, I finally tried another tactic which solved the problem. Those while loops certainly do want to have an exit condition in order to process.

Throughout the script, descriptive comments were added. After the script was completed, header comments were included to identify the script name, author, date, and a brief description of the script. This was a great practice exercise and assignment.

GIS4102 Module 3: Python Fundamentals Part 1

After last week's experience with scripting, this lab assignment was a breeze. Practicing within the exercise part of the module helped prepare for the assignment which involved starting with a string of my full name, splitting it into a list of names prior to printing the last name, and then determining the length of the last name. Mine is 13 ~ did anyone top that? Finally the length of the last name was multiplied by three. Trying to remember the functions and methods took some effort, but the book and instructions provided handy reference. I was most nervous about making sure that my name was spelled right, since it would be out there for all to see:

Results: Length of Last Name Times 3

The scripting was so fascinating that I ended up trying it out with the names of several friends and family members. I can tell that this is going to be a lot of fun... 

GIS4102 Module 2: Geoprocessing in ArcGIS

ModelBuilder in ArcMap was used to create a model designed to reduce a large soils file down to a much smaller area of land with soils suitable for farming. This was done using the clip process to reduce the area of concern down to a particular basin. The result of an SQL to select those soils not suitable for farming was then erased from the basin polygon. The results of the geoprocessing are shown here: 

Areas Suitable for Farming

Prior to making the model, workspaces were identified which kept the saving of the outputs in the same location and sped up the entire process. Making the model itself was quite intuitive and easy to do within ArcMap by dragging tools into ModelBuilder as needed and then having prompts for features and output. After the model was constructed the input and output variables were all set as Model Parameters which give the option to change the input features or output name and filepath. The model was saved and named before being exported as a Python script to be run in PythonWin. That's when my troubles began....

Executed in PythonWin, the script generated a number of errors, apparently more than just those noted in the assignment instructions. Updating the input lines to correct for the script being unable to find the input parameters was unsuccessful as were other suggestions recommended in the discussion board. This was an exercise in eye-straining scrutiny trying to find an extra space or typo of some sort that would prevent the script from running to completion. Something that was noted for future models exported to Python Script is the importance of taking screenshots of script and error messages before making changes...at least while in the learning process. Although the script was not completed to success, the learning process was valuable, and the script will be figured out with some additional help. 

GIS4102 Module 1: Introduction to Python

Not nearly as intimidating as initially expected, this module provided a history of Python and walk-through examples of using Python in different editors. For the remainder of the class, PythonWin will be the editor for coursework. Working in the interactive window will enable beginning programmers like me to see immediate results of scripting until becoming skilled enough to write more complex code as a script that will be saved. The syntax highlighting will also be beneficial in staying organized and consistent with the scripting.

Course Folder and Subfolders Created by the Script

The provided script in the assignment portion of this module was developed to create a course folder with module subfolders. The script ran in the blink of an eye, easily demonstrating the value of such a script when compared to creating each folder manually. There are so many valuable applications of such automation in GIS work! Shown at the right is a screenshot of the folder structure established by the script.

For someone whose last programming experience was Fortran, this was a great start to great programming opportunities.