Supplement 1. MATLAB function files for modeling Macoma balthica populations, and trophic transfer under normoxic and hypoxic conditions.

File List 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) Description <b>MbPopModel.m-</b> This MATLAB function will model the population of <i>Macoma balthica</i> 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:<br> param- A vector with five parameters: <i>MN</i>, <i>MH</i>, <i>RH</i>, <i>RN</i>, <i>d</i><br> Where <i>M</i> is the proportion of the juvenile population that reproduces in their first year, and <i>R</i> is the number of recruits produced by each female, and d is the areal proportion of the river that remains normoxic. Inits(<i>JN</i>, <i>AN</i>, <i>JH</i>, <i>AH</i>)- A vector with the initial population density of the Juveniles (<i>J</i>), and Adults (<i>A</i>) in the normoxic (subscript <i>N</i>) and hypoxic (subscript <i>H</i>). J- the number of years the model is to be run for. Base parameter estimates used in the paper are: -- TABLE: Please see in attached file. -- <b>Pop_and_Pred.m</b>- This MATLAB function will model the population (output <i>pop</i>) of <i>Macoma balthica</i> and provide an annual estimate of the biomass (output <i>B</i>) and number (output <i>N</i>) of clams consumed by blue crabs (<i>Callinectes sapidus</i>) 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:<br> Mparam- A vector with five parameters: <i>MN</i>, <i>MH</i>, <i>RH</i>, <i>RN</i>, <i>d</i><br> Where <i>M</i> is the proportion of the juvenile population that reproduces in their first year, and <i>R</i> 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: <i>tH</i>, <i>mH</i>,<i> P</i><br> Where <i>tH</i> is the duration of hypoxia in days, <i>mH</i> is the non-predatory mortality rate in hypoxic areas and <i>P</i> is the proportional increase in predation under hypoxic conditions. p&gt;Inits(<i>JN</i>, <i>AN</i>, <i>JH</i>, <i>AH</i>)- A vector with the initial population density of the Juveniles (<i>J</i>), and Adults (<i>A</i>) in the normoxic (subscript <i>N</i>) and hypoxic (subscript <i>H</i>). J- the number of years the model is to be run for. Base parameter estimates used in the paper are: -- TABLE: Please see in attached file. -- <b>dA.m</b>- Sub-function of MbPopModel and Pop_and_Pred that creates a population projection matrix using input parameters. <b>typeIII</b>- 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. <b>typeIIIH</b>- 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. <b>typeIII_P</b>- 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. <b>typeIIIH_P</b>- 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.