Difference between revisions of "User:Amohr07"

Latest revision as of 06:25, 12 June 2015

Anna Mohr

Hey guys! I'm Anna Mohr and I'm lucky enough to be completing my second REU project at Marquette. I'm a Computational Math major and plan on graduating in May 2011 but am seriously considering going to graduate school for Math next fall.

Summer 2010 Research

In the summer of 2010, I am researching risk modeling for pyroclastic volcano flows with Dr. Spiller. The following is a record of my work on the project, thus far. For more information, see the project description.

Goals/Objectives

Learn and become comfortable with R as a programming language
Understand Sacks' and Welch's Random Function Model (RFM)
Apply the RFM to a computationally expensive Pyroclastic Volcano Flow model

Week One (6/1)

attended REU initial group meeting and research practices talk
reading (and working through exercises in) chapters 1-4 of Jones, Owen, Robert Maillardet and Andrew Robinson. Introduction to Scientific Programming and Simulation Using R. New York: CRC Press, 2009.
initial read of Sacks, Jerry and Will Welch. The Random Function Model. Summer School on the Design and Analysis of Computer Experiments. 11-12 Aug 2006.

Week Two (6/7)

attended REU working lunch
working through chapters 4-8 of Jones, read and browsed examples for remaining chapters, 9-22
practiced programming in R with problems from Statistics textbook
more in-depth read of Sacks, researching questions and shaky concepts for better understanding
final write-up of notes on Sacks

Week Three (6/14)

met with Dr. Spiller to solidify understanding of Sacks
wrote a program in R to reproduce results of Sacks' example (RFpractice.r)

- achieved various non-conditional realizations of a RF

- achieved the conditional realization of a RF, with ability to manipulate beta, theta, alpha, and variance

- need to investigate: problems with size of Z(x) in RF.r and adding 95% CI to the conditional RF

Week Four (6/21)

no work this week - vacation with family in north carolina :)

Week Five (6/28)

re-familiarizing myself with previous work and code
added comments to previous code for better readability and to allow future adoptability
located and remedied minor glitch in code
began initial work for mini-presentation (7/9)
met with Dr. Spiller to gain better understanding of project goals

Week Six (7/5)

began incorporating Dancik, Garrett. "mlegp: an R package for Gaussian process modeling and sensitivity analysis." 5 November 2009.

- installed mlegp package for R

- mlegp package finds best theta and mu values for an RF, among other things

- achieved implementation of these two features (mlegpPractice.r)

met with Dr. Spiller to gain better understanding of original volcanic model
prepared and gave a presentation to REU students and mentors on my work thus far

Week Seven (7/12)

waiting for data from original volcanic model...
began gathering notes for final paper/poster/presentation

Week Eight (7/19)

still waiting for data from original volcanic model...
continuing working on preliminary work for final paper/poster/presentation

- wrote introduction and section on RF Modeling

finalizing plans for Vancouver trip!

Resources

Jones, Owen, Robert Maillardet and Andrew Robinson. Introduction to Scientific Programming and Simulation Using R. New York: CRC Press, 2009.
Sacks, Jerry and Will Welch. The Random Function Model. Summer School on the Design and Analysis of Computer Experiments. 11-12 Aug 2006.
Dancik, Garrett. "mlegp: an R package for Gaussian process modeling and sensitivity analysis." 5 November 2009.

Summer 2009 Research

In the summer of 2009, I researched the possible spread of Foot and Mouth Disease in Wisconsin Dairy Cattle with Bridget St.Peter, Alex Heaton, and Dr. Factor. The following is a tabulation of my weekly work on the project. For more information, see the project description and the final poster.

Week One (5/18)

MAY 18TH

Tried to obtain list of dairy farms in Sheboygan, utilizing government websites
Began preliminary perusal of the following helpful websites
USDA Agricultural Census
Sheboygan County Land Use
Time: 2 hours

MAY 19TH

Continued efforts to ascertain list of farms
Contacted USDA - legal restrictions, rerouted to Farm Service Agency, Agricultural Marketing Association
Contacted Farm Service Agency - call back Wed. am : 920.467.9917
Contacted UW Extension in Sheboyagn - left voicemail : 920.459.5900
Began downloading aerial map of Sheboygan from USDA Geospatial Data Gateway
Time: 4 hours

MAY 20TH

Read and took notes on articles from Alex's page:

Time: 4.5 hours

MAY 21ST

Obtained list of Sheboygan farms and discussed possible mechanisms by which to graphically represent farm locations
Further discussed methods by which to differentiate our research from previous academic work
Time: 1.5 hours

MAY 22ND

Met with Dr. Factor to discuss project focus and details
Began work on more detailed project proposal
Investigated method by which to capture geographic information of farm locations
Time: 3.5 hours

MAY 24TH

Finished program to format geographic information of farm locations
Developed program to calculate distances between farms
Time: 3 hours

Week Two (5/26)

MAY 26TH

Finalized project proposal
Distributed plotting program and instructions to group members
Manipulated distance program to output distances in kilometers, adjusted code from Movable Type Scripts
Completed initial version of graphing program
Time: 7.5 hours

MAY 27TH

Began reading Introduction to Graph Theory

consider using a digraph to represent truck routes, etc.
possibly examine disparity between longest path (weighted for probability) and geographical distance between two farms
investigate importance of the existence of cycles - would this make the virus more virulent?

Worked through proof of Domination to Bipartite Domination Theorem from Algorithmic Graph Theory, p81
BRAIN BURST:

use probability-weighted edges to determine testing sites
use time-weighted edges to determine testing frequency
both analyses would utilize the same factors, but different calculations to determine the weights

Compiled master list of farm locations in latitude and longitude coordinates
Continued work on graphing program, adding plotting functionality and beginning work on infection simulation functionality
Time: 6.5 hours

MAY 28TH

Met with group and discussed project goals
Continued work on finalizing a list of factors to consider

possibly designate some factors as more dangerous to spread outside of the region under consideration (i.e. Sheboygan county)

Time: 3 hours

MAY 29TH

Toured A-OK Farm in Sheboygan

need to further investigate influence of heifer growers, pig farm locations
consider including the influence of daily farm traffic - milk tankers, feed trucks, machinery service men, etc.

Continued work on graphing program, adding infection simulation functionality (for a single or all farms)
Time: 8 hours

Week Three (6/2)

JUNE 2ND

Discussed possible methods for finding and evaluating minimum dominating sets
Determined and outlined remaining major research tasks
Began identifying scholarly support for factors to be included in analysis - examining more recent sources that site these articles

Time: 4 hours

JUNE 3RD

Began reading Accuracy of Models for the 2001 Foot-and-Mouth Epidemic, to find support for factors to include in closeness analysis
Began organizing closeness data
Time: 1 hour

JUNE 4TH

Continued previous reading, for more closeness support
Focused on Accuracy of Models for the 2001 Foot-and-Mouth Epidemic, published in 2008
Time: 5 hours

Week Four (6/9)

JUNE 9TH

Continued previous reading
Reviewed original report (from Fall 2008), especially examining section on closeness
Time: 3 hours

JUNE 10TH

Reviewed new methods for finding dominating sets with Alex
Finished organizing thoughts on "closeness", e-mailed rough outline to group
Possible future tasks for determining closeness (if deemed valuable):

Find plot size of each farm using the Sheboygan County Real Estate Lookup
Estimate average current on coast of Lake Michigan

Settling Particle Fluxes, and Current and Temperature Profiles in Grand Traverse Bay, Lake Michigan - see data on currents from Appendix II, needs to be averaged
GLERL Great Lakes Monthly Hydrologic Data - see data on channels in "Annonymous FTP" section, need to estimate values for St.Mary's in 2009 (regression line)
Lake Michigan in Motion

Find values for currents on major rivers, boat traffic on rivers and lakes, speed limits on major roadways and railways, average traffic on major roadways and railways, population density
Quantify seasonal variation

Began organizing programs - defined Matrix class and a Graph class which extends Matrix
Time: 8 hours

JUNE 11TH

Met with group and discussed remaining tasks
Finished analysis of factors - currently using only Euclidean distance
Continued work on programs

Added 'input from file' functionality to new suite of programs
Began work on scaling of distances

Began reading A Java Library of Graph Algorithms and Optimization (2007)
Time: 4.5 hours

JUNE 12TH

Discussed and resolved issues of over-connectedness

Methods to determine approximate dominating set, not neccessarily minimum dominating set
Possible importance in other applications
Decrease cull range based on consumer's varying intended degrees of risk

Continued work on programs

Finished scaled adjacency matrix
Began work on first method of finding an approximate dominating set - OWN, Order Weighted Neighborhoods (need to add methods to replace members of the dominating set that are multiple path lengths away from each other)

Perused A Java Library of Graph Algorithms and Optimization, examining included media CD of code
Time: 4 hours

Week Five (6/15)

JUNE 15TH

Continued to work on programs

Adjusted previous work to replace by moving up in list
Added method to check new members of list with previously checked members
Eliminated unneccesary calculations

Time: 5.5 hours

JUNE 16TH

Continued work on programs

Created Version #2 of OWN, to verify results
Added graphing functionality - produces a graph which circles the members of the produced dominating set

Time: 6 hours

JUNE 17TH

Briefly began work on spanning trees method

Need to further research creating a random spanning tree from a graph
Discussed importance of minimum (or maximum) spanning trees
Read A Java Library of Graph Algorithms and Optimization, p.14, 75

Began work on jumping method

Made Sorted class, for use in both OWN and Jump tests
Set up user-indicated starting point
Wrote method to find next edge with lowest weighted value

Time: 10 hours

JUNE 18TH

Met as a group with Dr. Factor to present progress thus far
Added indices and indicator arrows to graphing program, both optional
Worked with Alex to understand Customized Vertex Value Method
Began programming CVVM

Created outline of class, variable types, and a few general methods
Set up tester program to run versions of CVVM as I continue to code it

Time: 7 hours

JUNE 19TH AND 20TH

Continued work on CVVM code
Continued reading from A Java Library of Graph Algorithms and Optimization
Time 2 hours

Week Six (6/21)

Please note that during this week, I am on vacation and am working significantly reduced hours.

JUNE 21ST

"Finished" programming CVVM (Customized Vertex Value Method)

Added all functionalities as discussed with Alex
User must input sum intervals and values as well as closeness intervals and values
Needs to be double-checked, probably by hand

Time: 3 hours

JUNE 23RD

Double-checked CVVM by hand, utilising a smaller example graph

Ironed-out kinks in program, including faulty sorting method

This process should be repeated for all previously coded tests, just in case
Initial results of CVVM provided relatively "close" dominating sets - needs to be discussed and input parameters need to be adjusted (i.e. play around with it)
Time: 3 hours

JUNE 24TH

Used previously developed tester to double-check OWN and JUMP programs

Verified application to smaller scale graphs
Ironed out small kinks, including making closeness ranges inclusive (rather than exclusive)

Need to develop more test cases to check programs
Time: 3 hours

JUNE 26TH

Continued debugging and developing test cases
Modified OWN to output more helpful information, in terms of debugging
Time: 3 hours

JUNE 28TH

Met with group to catch up on their research activities over the past week
Went through PowerPoint presentation for Thursday
Began initial discussions of the final paper
Disambiguated terms from the CVVM method
Time: 2 hours

Week Seven (6/27)

JUNE 29TH

Updated programs to refelct yesterday's group discussion
Zipped and adjusted programs for use by Alex and Bridget on other computers
Time: 2 hours

JUNE 30TH

Worked on outputting a jpg image, problems with colors
Time: 2.5 hours

JULY 1ST

Fixed color problem of jpg images, changed save location to user input
Coded first testing method (minDist), for evaluating the "goodness" of a dominating set
Split up Main program into methods
Performed MAJOR debugging of programs

Adjusted code to allow for use on other computers (i.e. generalized save location)
Fixed minDist test
Finished CVVM, should be fully functional now

Helped Bridget run programs on her desktop
Time: 11 hours

JULY 2ND

Finished up presentation
Attended Mid-Summer Presentation/Luncheon - really great to learn about others' (incredible) work and research
Time: 4 hours

JULY 3RD

Began investigating coding additional tests (for evaluating "goodness" of dominating sets)
Time: 3 hours

JULY 5TH

Coded tentative version of Test #2 - Minimum Weighted Path
Need to double check how program should "choose" path
Time: 2.5 hours

Week Eight (7/6)

JULY 6TH

Updated Test #2 to choose paths based on probability (not simply weights)
Also added back spread capability to Test #2
Test #2 requires further testing
Time: 5 hours

JULY 7TH

Began working on gui for program - should speed up data entry and analysis
Requires much further development and finetuning
Time: 5 hours

JULY 8TH

Discussed data systemization with Bridget - need to develop program to run suite of tests (approx. 2000 runs of JUMP method alone)
Continued work on GUI

OWN is presumably functioning correctly - requires further verification
Need to work on displaying output in a meaningful fashion

Time: 3 hours

Week Nine (7/13)

JULY 13TH

Put finishing touches on initial version of GUI
Began coding program to run high quantities of iterations for data analysis - OWN complete
Time: 5.5 hours

JULY 14TH

Briefly reviewed results of running many iterations of OWN
Worked with Bridget to eliminate a possible additional method
Time: 4 hours

JULY 15TH

Began working on JUMP in bulkRun program - allows for user-specified entry of 2 fixed variables
Finished JUMP in bulkRun program
Time: 4 hours

JULY 16TH

Worked with Bridget to address data collection and analysis issues
Finished second goodness test - needs to be implemented into Main and bulkRun programs
Worked to implement second goodness test in bulkRun program - needs further finetuning
Time: 6.5 hours

JULY 17TH

Continued implementing second goodness test into bulkRun and Main programs
Made dominating sets of requested size 0 special cases in second goodness test and jump programs
Worked with Alex to create more meaningful output from bulkRun programs
Began recoding bulkRun program with simpler method for fixing variables in JUMP method
Created brief program to print ranges of indices on a map of the farms
Continued work with recoding of bulkRun programs - need to devise simple method for labeling results in Jump Output...
Time: 10 hours

JULY 18TH

Finished new bulkRun programs

Added more descriptive headings
Incorporated second goodness test
Added capability of printing out sizes of dominating sets

Time: 5 hours

JULY 19TH

Coded fourth method for finding a dominating set - Probability Method

needs further fine-tuning, especially in choosing which vertex of the combined vertex to include in the dominating set

Time: 5.5 hours

Week Ten (7/20)

JULY 20TH

Finished coding fourth method
Began integrating fourth method into Main program
MinWeightedPath is no longer working, needs a lot of work...
Fixed Probability Method program, which eliminated problems with MinWeightedPath
Began coding Path Length Two Method
Time: 8 hours

JULY 21ST

Continued work on Path Length Two Method
Need to determine what happens when the program chooses a vertex with no vertices that are at most path length two away
Finished Path Length Two Method, only requires a few more test runs
Time: 5 hours

JULY 22ND

Implemented Path Length Two Method into Main program
Coded bulk run program specifically for Path Length Two Method (since there is only one variable input)
Began initial examination of results of Path Length Two Method
Began coding Test #3 - need to clarify why a dominating set's neighbors would want to include each vertex only once...
Finished coding Test #3, remains to be integrated into Main program
Time: 8 hours

JULY 23RD

Integrated Test #3 into Main program
Decided to eliminate Test #4 from further consideration
Ran Bridget's test graphs through Jump - results confirm that the program is running accurately and has been successfully implemented
Realized and tried to fix problem in PLT Method - fixing requires further verification
Time: 5 hours

JULY 24TH

Worked on fixing problem in PLT Method
PLT currently works correctly within tester programs, but needs to be better implemented in the main program
Continued adjusting PLT
Time: 6 hours

JULY 25th

Adjusted PLT to allow full functionality in Main program
Time: 4 hours

JULY 26TH

Discovered issue with PLT method, for a cut off length of 0.94
Still working to fix this issue
Time: 6 hours

Week Ten (7/27)

JULY 27TH

Worked through PLT method with a cut-off value of 0.94 on the Sheboygan graph
Concluded that entire program needs to be adjusted to accomodate looking for vertices path length two away from those vertices that are path length two away from the starting vertex (and so on and so forth)
Time: 5.5 hours

JULY 28TH

Continued to manually work through PLT glitch
Realized that sorting method is faulty, fails to properly record the last item in the list if it has a value of zero
Fixed PLT method (finally!)
Time: 7.5 hours

JULY 29TH

Mapped plan of attack for bulk run program incorporating CVVM
Briefly began initial coding of above program
Time: 3 hours

JULY 30TH

Adjusted CVVM to allow bulk runs, restricted number of intervals to two each (closeness and disconnectedness)
Added CVVM to bulkMinDist and bulkRandPaths programs
Time: 8.5 hours

JULY 31ST

Read over other members' contributions to the paper
Worked on representing results for different methods via graphs in three dimensions
Time: 6 hours

AUGUST 1ST AND 2ND

Researched standard format for a scientific report: {http://umech.mit.edu/freeman/6.021J/2000/writing.pdf Writing a Scientific Research Paper - MIT]
Reread paper from fall semester
Briefly began writing introduction
Time: 5 hours

Week Eleven (8/3)

AUGUST 3RD

Discussed paper set-up and formatting
Began writing part of introduction and programming section
Time: 3.5 hours

AUGUST 4TH

Recoded PROBS method to allow for "skewing" the graph up or down
Implemented new version of PROBS into Main program
Added PROBS to bulkMinDist program - takes to long to run to add to bulkRandPaths
Time: 5 hours

AUGUST 5TH

Adjusted PROBS method to allow for the use of a cut-off value
Reimplemented PROBS into Main and bulkMinDist programs
Began reading compiled version of the paper
Finished most of introductory portion of computer programming nots
Compiled everything that we have for the paper so far into one document, with correct ordering and formatting
Time: 10 hours

AUGUST 6TH

Briefly adjusted bulkMinDist program for CVVM to more easily accomodate variations in closeness values
Began writing computer programming notes for specific methods and tests
Cleaned up code for programs, to be added to final paper
Time: 3.5 hours

AUGUST 7TH

Finished programming notes
Added codes for programs to appendix, fixed formatting
Compiled remainder of paper
Wrote conclusions section
Printed final paper!!
Time:8 hours

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