ATLSS Landscape Fish Model (ALFISH) Brief Description - November 1997
Donald DeAngelis, Holly Gaff, Louis Gross, Moris Shorrosh
The Institute for Environmental Modeling
University of Tennessee - Knoxville
Copyright 1998 - The University of Tennessee
The ATLSS Landscape Fish model (ALFISH) has as its main objective the
ability to compare in a spatially-explicit manner the relative effects
of alternative hydrologic scenarios on fresh-water fish densities
across South Florida. Another objective is to provide a measure of the
dynamic, spatially-explicit food resources available to wading birds.
ALFISH operates by splitting the landscape into spatial grid cells, of
size 500 m by 500 m, characterizing the within-cell variability in
water depth in a statistical manner. Within each cell, there is a
distribution of elevations based upon an average hypsograph obtained by
averaging data from a number of locations. Cells also contain
permanently wet areas of small size, called ponds, with the remaining
cell areas which may be subject to periodic dry down and reflooding
called the marsh areas. Fish densities change within cells between
areas of various depths as a cell drys down or rewets, since differing
fractions of area within cells will be at differing water depths. The
spatial cells are coupled in the model by movements of fish density
between cells due to differences in relative fish densities or
differences in relative water depth between cells. ALFISH is a mostly
deterministic model, with the only stochastic component being the
the size of the pond within each cell.
The main inputs to ALFISH are hydrology data at a 500 m resolution from
the pseudotopography model, time of year, and food resources available
from lower trophic levels. For the current application of ALFISH to the
Restudy, all lower trophic level resources are assumed constant,
independent of hydrology. The time step of the model is 5-days, so
hydrology data is averaged to produce 5-day average water depths for
each 500 m cell across the study area. The study area includes all of
the region for which hydrology data are being produced for each scenario,
with some outputs being computed only for particular sub-regions within
the study area.
ALFISH considers two fish functional groups: Functional Group #1 (small
fish) includes all fish species which have a maximum possible length in
the system of 7 cm; Functional Group #2 (large fish) includes all fish
species with maximum lengths of greater than 7 cm. For example, the
model would consider Killifishes or small live-bearers (Poeciliids) to
be in functional group #1, while Gar and catfish would be in functional
group #2. ALFISH treats the fish functional groups as an age-size
structured model. Each age class is 30 days. The Large Fish functional
group has 40 age classes, while the Small Fish functional group has 25
age classes. The Large Fish functional group has two stages: the first
stage includes the first few age classes when fish are small in size
and can be preyed upon by the second stage of larger, older fish. Each
age class is divided into 6 size classes with length (in cm) calculated
as a function of age from a Von Bertalanffy equation.
The fish in each functional group grow in size every 5-day time step,
and move to the next age class every 30 days. Mature fish of each
functional group produce a number of viable offspring during their
reproductive month. The age of maturity, the fecundity, and the months
during the year in which each functional group reproduces are
parameters which can differ for each functional group. Currently, only
the age of maturity and the fecundity are unique to each functional
group. For both functional groups, it is assumed that they can
reproduce at the first time step of every month. There are four causes
of mortality in ALFISH: (i) Background mortality, or the natural
mortality of an uncrowded population, which is dependent on fish age
class, but is independent of population size; (ii) Density-dependent
mortality from starvation; (iii) Loss due to predation from other
functional groups; and (iv) Death due to dry down in which some fraction
of fish density do not successfully reach deeper water as a cell drys.
Movement in ALFISH has two phases. First, within cell movement takes
place allowing fish density to move between the pond and the marsh
areas of various depths within a particular cell. Secondly, fish
density can shift between the marsh areas of adjoining cells, based on
differences between water depth and fish densities in these cells. When
the fraction of a cell with standing water has dropped too low, it is
assumed there is no longer movement of fish into or out of that cell.
While ALFISH is capable of producing very detailed comparisons of
changes in fish densities and size structure between scenarios, the
outputs being placed on the ftp site for distribution are just a small
fraction of what it produces. All of the outputs on the ftp site
concern just the Small Fish functional group. The ALFISH outputs for
the Restudy posted to the ftp site are:
(1) Maps of the Small Fish functional group total number density (#
fish/ m^2) in the marsh areas within cells over the entire region
modeled at a 500 m x 500 m cell resolution generated for a single day
at two times (model time step dates nearest July 1 and October 15).
These maps will be produced for three years over the course of the
simulation: a high, average, and low rainfall year.
(2) Maps of the Small Fish functional group total number density (#
fish/ m^2) in the marsh areas within cells of fish > 2cm length over
the entire region modeled at a 500 m x 500 m cell resolution generated
for a single day at three times during wading bird breeding season
(January 1, February 15, and April 1) in cells with appropriate water
depth for wading bird foraging (10 cm to 30 cm water depth). These maps
will be produced for three years over the course of the simulation: a
high, average, and low rainfall year.
(3) Maps of average Small Fish functional group total number density (#
fish/ m^2) in the marsh areas within cells over the entire 31 year
scenario for these dates, with the July 1 and October 15 maps including
fish of all size classes, and the January 1, February 15, and April 1
maps including just fish densities for those size classes > 2cm. These
maps are all for the entire region, not just portions with certain water
depths.
(4) Time series showing the average number density of the Small Fish
functional group, averaged over the entire region, with output every 2
model time steps (e.g. every 10 days). Separate time series for fish
densities in marsh and in pond areas.
(5) Time series showing the average number density of the Small Fish
functional group (# fish/ m^2), for fish between 2 and 7 cm length,
associated with each of the wading bird breeding season maps in (2)
above. Time step for these series is every 5 days over the breeding
season from December 15 to May 15, with separate time series for each
of the maps described in (2) and for the 31-year average map described
in (3).
(6) Time series showing the average number density of the Small Fish
functional group in two subregions of WCA 3A (a long-hydroperiod and a
short hydroperiod subregion, derived based upon empirical observations
by Joel Trexler), with output every 2 model time steps (e.g. every 10
days), for fish between 2 and 7 cm length.
(7) Time series of histograms of the size distribution of the Small
Fish functional group in the marsh areas of the two subregions of WCA 3A
described in (6), with output every model step (e.g. every 5 days).
(8) Tables summarizing the total fish number densities broken down by
basin area and by year. The entries represent fish per meter squared
averaged over the entire year.
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Outputs associated with the ATLSS Landscape Fish Model (ALFISH)
In accordance with the ATLSS file naming conventions,
each file name consists of the characters:
"F","E", or "_" => F = the Future Without Project Condition (2050 Base)
E = Existing Condition (C1995 Base)
_ = No Base condition, a run of a scenario only
"0-9, A-Z" or "_" => Scenario Identifier (e.g. 0 = Scenario 0)
_ = No Scenario, a run of Base case only
"FI" => the ATLSS Fish Model
"XXXX" => 4 character mnemonic
"."
"PDF" or "TXT" or "DOC" => PDF, tabular text or documentation
Note: For all output, fish means only those in the Small Fish
Functional Group (Functional Group #1). In addition, "total fish"
means all fish are counted in all water depths. "Fish available for
wading birds" means only fish greater than 2 cm in length found in
water between 10 and 30 cm deep are counted. "Fish over 2cm long in
all water" is used for only for maps which average the model output
over several years. The units for all three are numbers of fish per
meter squared.
1. Maps
The map outputs used to characterize the results of
the ATLSS Fish Model will consist of 20 map images
in the PDF file format. Each map shows a "Set" of model
results, comparing a Base case to a Scenario, following the
conventions for ATLSS comparison of two model runs.
Each map has 3 panels. The left panel is the alternative
scenario. The right panel is the base scenario - typically the
Future without Project Conditions Case. The middle panel is the
difference between the two scenarios.
For each of five dates during a high, low and average rainfall
year the images provide a spatial display of the density of fish
available for wading birds or total fish available upon that day.
October 15 and July 1 display the total fish available on the model
date closest to these in that year. The outputs for the other dates
display only the fish available for wading birds. In addition, there
are maps for the five dates averaged over 31 years of the run. These
averages are total fish for the October 15 and July 1 dates, and fish
over 2cm long in all water depths for the other three dates.
The mnemonic characters are composed according to
the convention:
"XX" = Last two digits of the year or "MY" for the Mean
value of all years.
"XX" = D1, D2, D3, D4, D5 -> the date designator
Listing of ALFISH map files for 2050 Base compared to Alternative 0:
File Name Type of Year Closest Model Time Step to Day
------------ ------------------- ------------------------------
XXFI68D1.PDF High Rainfall Oct. 15
XXFI69D2.PDF High Rainfall Jan. 1
XXFI69D3.PDF High Rainfall Feb. 15
XXFI69D4.PDF High Rainfall Apr. 1
XXFI69D5.PDF High Rainfall Jul. 1
XXFI76D1.PDF Average Rainfall Oct. 15
XXFI77D2.PDF Average Rainfall Jan. 1
XXFI77D3.PDF Average Rainfall Feb. 15
XXFI77D4.PDF Average Rainfall Apr. 1
XXFI77D5.PDF Average Rainfall Jul. 1
XXFI89D1.PDF Low Rainfall Oct. 15
XXFI90D2.PDF Low Rainfall Jan. 1
XXFI90D3.PDF Low Rainfall Feb. 15
XXFI90D4.PDF Low Rainfall Apr. 1
XXFI90D5.PDF Low Rainfall Jul. 1
XXFIMYD1.PDF Average of all Years Oct. 15
XXFIMYD2.PDF Average of all Years Jan. 1
XXFIMYD3.PDF Average of all Years Feb. 15
XXFIMYD4.PDF Average of all Years Apr. 1
XXFIMYD5.PDF Average of all Years Jul. 1
========================================================
2. Time Series Charts
The time series charts associated with ALFISH consists of the
following files:
File Name Description
------------ ------------------------------------------------
XXFIAVGD.PDF The total fish density in marsh and pond every
10 days averaged across the entire area.
XXFIBRY1.PDF The fish available for wading birds in 10-30cm water
for Dec 15, 1968 through May 15, 1969.
XXFIBRY2.PDF The fish available for wading birds in 10-30cm water
for Dec 15, 1976 through May 15, 1977.
XXFIBRY3.PDF The fish available for wading birds in 10-30cm water
for Dec 15, 1989 through May 15, 1990.
XXFIAVGB.PDF The fish longer than 2cm in all water depths averaged for
every year for Dec 15 through May 15.
XXFILHAB.PDF The total fish in a long hydroperiod subregion of
WCA 3A across all years. The two subregions together
cover all of WCA 3A, are fixed throughout all model
runs, and are derived from empirical estimates by
Joel Trexler.
XXFISHAB.PDF The total fish in a short hydroperiod subregion of
WCA 3A across all years. The two subregions together
cover all of WCA 3A, are fixed throughout all model
runs, and are derived from empirical estimates by
Joel Trexler.
3. Histograms
The histograms associated with ATLSS Fish Model display
the size distribution of fish within two subregions of WCA 3A
corresponding to long and short hydroperiods based upon empirical
estimates by Joel Trexler, and give the fish size structure dynamics
corresponding to the total fish data in file shown in XXFILHAB.PDF.
Each image displays the size structure dynamics for half the years
of the run. The histograms consist of the following files:
File Name Description
------------ ------------------------------------------------
X_FIBLH1.PDF A size histogram for fish in the long hydroperiod
subregion in WCA 3A in the indicated base scenario
and the first half of the years of the run.
X_FIBLH2.PDF A size histogram for fish in the long hydroperiod
subregion in WCA 3A in the indicated base scenario
and the second half of the years of the run.
_XFIALH1.PDF A size histogram for fish in the long hydroperiod
subregion in WCA 3A in the indicated alternative
scenario for the first half of the years of the run.
_XFIALH2.PDF A size histogram for fish in a the long hydroperiod
subregion in WCA 3A given the indicated alternative
scenario for the second half of the years of the run.
X_FIBSH1.PDF A size histogram for fish in the short hydroperiod
subregion in WCA 3A in the indicated base scenario
and the first half of the years of the run.
X_FIBSH2.PDF A size histogram for fish in the short hydroperiod
subregion in WCA 3A in the indicated base scenario
and the second half of the years of the run.
_XFIASH1.PDF A size histogram for fish in the short hydroperiod
subregion in WCA 3A in the indicated alternative
scenario for the first half of the years of the run.
_XFIASH2.PDF A size histogram for fish in the short hydroperiod
subregion in WCA 3A in the indicated alternative
scenario for the second half of the years of the run.
4. Tables
The tables associated with the ATLSS fish model consist of the
following files:
File Name Description
------------ ------------------------------------------------
F_FIBASE.TXT Total fish listed by years and basin areas for
the Future Without Project Condition scenario.
_XFIBASE.TXT Total fish listed by years and basin areas for
the indicated scenario.
FXFIDIFF.TXT The difference of the total fish listed by years
and basin areas between the Future Without Project
Condition and the indicated scenario.