W. Christopher Long
Kodiak Laboratory, NOAA Alaska Fisheries Science Center
301 Research Court
Kodiak, AK 99615 USA
E-mail: Chris.Long@noaa.gov

Rochelle D. Seitz
Virginia Institute of Marine Science, College of William & Mary
P.O. Box 1346
Gloucester Pt., VA 23062 USA

Bryce J. Brylawski
Albright College
P.O. Box 15234
Reading, PA 19612 USA

Romuald N. Lipcius
Virginia Institute of Marine Science, College of William & Mary
P.O. Box 1346
Gloucester Pt., VA 23062 USA

MbPopModel.m (MD5: fbf47bb585a7f041100da16138dc8ab0)

Pop_and_Pred.m (MD5: 435f0942c819b03520e41bea6ec7756e)

dA.m (MD5: 67e503d79e2373c3756d7eb322ae4a84)

typeIII.m (MD5: 3664dfa10b84d28960b8bd952e66e058)

typeIIIH.m (MD5: 7cc47c1e7de06bbf7fb824bcdb03b6e8)

typeIII_P.m (MD5: dc445d6b130c070b8f73ffbb9779b08f)

typeIIIH_P.m (MD5: f5cf34d4a88340c688394a1be50f9ad7)

MbPopModel.m- This MATLAB function will model the population of Macoma balthica over a user specified length of time. Required sub-functions that are called within this function are dA.m, which creates a population projection matrix using input parameters and tyepIII.m and typeIIIH.m which are a series of linked ordinary differential equations describing the population dynamics during the summer in normoxic and hypoxic areas of the river.

The three inputs to the function are:
param- A vector with five parameters: MN, MH, RH, RN, d
Where M is the proportion of the juvenile population that reproduces in their first year, and R is the number of recruits produced by each female, and d is the areal proportion of the river that remains normoxic.

Inits(JN, AN, JH, AH)- A vector with the initial population density of the Juveniles (J), and Adults (A) in the normoxic (subscript N) and hypoxic (subscript H).

J- the number of years the model is to be run for.

Base parameter estimates used in the paper are:

Parameter	Estimate
MN	0.06
MH	0.34
RN (recruits clam-1)	10
RH (recruits clam-1)	6
d	0.6

 

Pop_and_Pred.m- This MATLAB function will model the population (output pop) of Macoma balthica and provide an annual estimate of the biomass (output B) and number (output N) of clams consumed by blue crabs (Callinectes sapidus) and those that suffer non-predatory mortality. Required sub-functions that are called within this function are dA.m, which creates a population projection matrix using input parameters and tyepIIIP.m and typeIIIH_P.m which are a series of linked ordinary differential equations describing the population dynamics during the summer in normoxic and hypoxic areas of the river.

The four inputs to the function are:
Mparam- A vector with five parameters: MN, MH, RH, RN, d
Where M is the proportion of the juvenile population that reproduces in their first year, and R is the number of recruits produced by each female, and d is the areal proportion of the river that remains normoxic.

Param- A vector with three parameters: tH, mH, P
Where tH is the duration of hypoxia in days, mH is the non-predatory mortality rate in hypoxic areas and P is the proportional increase in predation under hypoxic conditions.

p>Inits(JN, AN, JH, AH)- A vector with the initial population density of the Juveniles (J), and Adults (A) in the normoxic (subscript N) and hypoxic (subscript H).

J- the number of years the model is to be run for.

Base parameter estimates used in the paper are:

Parameter	Estimate
mH (days-1)	0.001
Th (days)	90
MN	0.06
MH	0.34
RN (recruits clam-1)	10
RH (recruits clam-1)	6
d	0.6
P	3.0

 

dA.m- Sub-function of MbPopModel and Pop_and_Pred that creates a population projection matrix using input parameters.

typeIII- Sub-function of MbPopModel that is a series of linked ordinary differential equations describing the population dynamics during the summer in normoxic areas of the river.

typeIIIH- Sub-function of MbPopModel that is a series of linked ordinary differential equations describing the population dynamics during the summer in hypoxic areas of the river.

typeIII_P- Sub-function of Pop_and_Pred that is a series of linked ordinary differential equations describing the population dynamics and predation during the summer in normoxic areas of the river.

typeIIIH_P- Sub-function of Pop_and_Pred that is a series of linked ordinary differential equations describing the population dynamics and predation during the summer in hypoxic areas of the river.