Bugs About Bugs
Not those, the other kind.
Welcome! This site has information about the SharpHog Southern
Pine Beetle Infestation Model and the related Spot-Growth
Database.
The SharpSpb project is comprised of two components. The
SharpHog infestation computer-model, and the Spot-Growth
Database.
SharpHog is a mathematical model of a biological system.
Specifically, SharpHog models Southern Pine Beetle
Infestations in the forests of the American South East.
SharpHog continues the evolution of the HogModel, an original
written in FORTRAN, then translated and upgraded over the
decades--most recently the JavaHog translation. SharpHog is written
in C# 2008 using the .NET 3.5 Framework, but is
platform-independant in its exposed interface, which uses Xml.
The SharpSpb Spot-Growth Database is a well-defined, using
international standards, schema, or structure, for entomological
field and experimental data concerning the Southern Pine Beetle.
Information about actual infestatons of SPB has been gathered
for decades, and taken many forms along the way. The
Spot-Growth Database normalizes and standardizes all known bits of
data that could be set for a Visit (on a date) to a Spot (a
location). As well as rigorously defining a strongly-typed
schema for the field data, multiple methods and interfaces were
created to facilitate transfer from the prior forms the data has
taken.
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Throughout this site I keep saying this or that X-including
acronym is an "international standard".
Specifically, these are the international standards adopted by the
SharpSpb project in both the Spot-Growth Database information
clearinghouse, and the SharpHog Southern Pine Beetle infestation
Model:
- XML - eXstensible Markup Language is a
set of rules for structuring information, and files that obey this
specification
- XSD - XML Schema Definitions describe
concretely the value-types, ranges, & data-relationships in a
particular XML file
- XSLT - eXtensible Stylesheet Language
Transformations style or transform the data in an XML file
- XPath - XML Path Language is the
specification for a shorthand used to traverse and examine an XML
tree.
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This article and its child articles discuss and illustrate a
possible workflow with SharpSpb.
Our goal for this exercise is to run the model on some real
field data based input, then compare the model's predictions from
this input set to the actual observed conditions in the field for a
given number of days elapsed. We only want a crude enough
output to confirm the model is behaving correctly--a true
statistical analysis of accuracy would involve many more Spots and
Vists. We just want to eyeball things.
Here's how we can achieve this. The Spot-Growth Database Administration
Application can read a great number of different file formats
representing actual Visits to actual Spots. A random
selection from a big pool of data files is loaded.
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The SharpHog computer model is an implementation in C# and Xslt
of an entire set of earlier southern pine beetle infestation
models. From an original written at the University of
Arkansas in FORTRAN in the 1970s, the original HogModel, as it was
dubbed, underwent a series of updates, additions, and
re-implementations. Recent translations to Java for an online
implementation at Virginia Tech (JavaHog),
and then to also to C++(COMHog), resulted in equivalent models to
the original, but the complexity had grown as well. Changes a
scientist might want to make to the HogModel in these forms were
laborious at best, and error-prone as a rule. Equations used
by the model to calculate reproduction, mortality rate, initial
population, and so on, were defined multiple times in the source
code,
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The Spot-Growth Database is slightly misnamed. It isn't a
database in the traditional single binary-file of relational
data accessed through special applications and query languages
sense. What the SharpSpb Spot-Growth Database is, is a
well-defined, using international standards, schema, or structure,
for entomological field and experimental data. Data from
decades of projects on dozens of doctorates from hundreds of actual
infestations stored on floppy disks and web servers and in paper
files can now be collected under one encompassing structure, and
this set of data can be maintained and its integrity verified by
scientists and administrators.
A single source of verified data that can be used to
demonstrate the accuracy of the model, or for other
applications.
The Spot-Growth Database is a set of inter-related
