| Title: | R Package for Aqua Culture |
|---|---|
| Description: | Solves the individual bioenergetic balance for different aquaculture sea fish (Sea Bream and Sea Bass; Brigolin et al., 2014 <doi:10.3354/aei00093>) and shellfish (Mussel and Clam; Brigolin et al., 2009 <doi:10.1016/j.ecss.2009.01.029>; Solidoro et al., 2000 <doi:10.3354/meps199137>). Allows for spatialized model runs and population simulations. |
| Authors: | Baldan D. [aut, cre], Palazzo D. [ctb], Porporato E.M.D [ctb], Brigolin D. [ctb] |
| Maintainer: | Baldan D. <[email protected]> |
| License: | MIT + file LICENSE |
| Version: | 1.5.5 |
| Built: | 2025-02-21 04:15:13 UTC |
| Source: | https://github.com/damianobaldan/rac |
Function that loads forcings data for Seabass individual bioenergetic model and performs the interpolation
Bass_ind_dataloader(userpath)Bass_ind_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Seabass bioenergetic individual model differential equations
Bass_ind_equations(Param, Temp, G, Food, weight)Bass_ind_equations(Param, Temp, G, Food, weight)
Param |
vector containing all metabolic parameters |
Temp |
water temperature forcing at time t |
G |
food entering the cage at time t |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
weight |
individual weight at time t |
model output at time t
Solves the bioenergetic balance for Seabass
Bass_ind_main(userpath, forcings)Bass_ind_main(userpath, forcings)
userpath |
the path where forcing are located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d] |
A list containing model outputs: weight, excreted quantities and quantities to waste, actual and potential ingestion, temperature limitation functions and metabolic rates
Seabass bioenergetic individual model postprocessor
Bass_ind_post(userpath, output, times, Dates, CS)Bass_ind_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Seabass |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Seabass bioenergetic individual model preprocessor
Bass_ind_pre(userpath, forcings)Bass_ind_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Solves the Seabass bioenergetic balance with a 4th order Runge Kutta method
Bass_ind_RKsolver(Param, Temperature, G, Food, IC, times)Bass_ind_RKsolver(Param, Temperature, G, Food, IC, times)
Param |
vector containing all metabolic parameters |
Temperature |
water temperature forcing time series |
G |
food entering the cage time series |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
IC |
initial conditions |
times |
vector containing integration extremes and integration timestep |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Creates the folders structure for Seabass individual bioenergetic model
Bass_ind_skeleton(userpath)Bass_ind_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Seabass population model and performs the interpolation
Bass_pop_dataloader(userpath)Bass_pop_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Seabass bioenergetic population model differential equations
Bass_pop_equations(Param, N, Temp, G, Food, weight)Bass_pop_equations(Param, N, Temp, G, Food, weight)
Param |
vector containing all metabolic parameters |
N |
the number of individuals at time t |
Temp |
water temperature forcing at time t |
G |
food entering the cage at time t |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
weight |
individual weight at time t |
model output at time t
Function that runs the Monte Carlo simulation for the Seabass population model
Bass_pop_loop(Param, Tint, Gint, Food, IC, times, N, userpath)Bass_pop_loop(Param, Tint, Gint, Food, IC, times, N, userpath)
Param |
a vector containing model parameters |
Tint |
the interpolated water temperature time series |
Gint |
the interpolated feeding rate time series |
Food |
the food characterization |
IC |
initial condition |
times |
integration extremes and integration timestep |
N |
time series with number of individuals |
userpath |
the path where the working folder is located |
a list with RK solver outputs
Seabass bioenergetic population model
Bass_pop_main(userpath, forcings)Bass_pop_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d] |
A list containing model outputs: weight, excreted quantities and quantities to waste, actual and potential ingestion, temperature limitation functions and metabolic rates
Postprocess the Seabass population bioenergetic model results
Bass_pop_post(userpath, output, times, Dates, N, CS)Bass_pop_post(userpath, output, times, Dates, N, CS)
userpath |
the path where the working folder is located |
output |
list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
N |
the number of individuals time series |
CS |
the commercial size of Seabass |
output: a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Seabass bioenergetic population model preprocessor
Bass_pop_pre(userpath, forcings)Bass_pop_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Solves the Seabass population bioenergetic balance with a 4th order Runge Kutta method
Bass_pop_RKsolver(Param, Temperature, G, Food, IC, times, N)Bass_pop_RKsolver(Param, Temperature, G, Food, IC, times, N)
Param |
vector containing all metabolic parameters |
Temperature |
water temperature forcing time series |
G |
food entering the cage at time series |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
IC |
initial condition on weight |
times |
integration times |
N |
number of individuals time series |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Creates the folders structure for Seabass population model
Bass_pop_skeleton(userpath)Bass_pop_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Bass spatialized model and performs the interpolation
Bass_spatial_dataloader(userpath)Bass_spatial_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Solves the bioenergetic balance for Bass
Bass_spatial_loop(userpath, forcings)Bass_spatial_loop(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
a list containing the outputs that main script saves to .nc; .csv and .asc files
Solves the bioenergetic balance for Bass
Bass_spatial_main(userpath, forcings)Bass_spatial_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
list containing the time series in the odd positions and realted forcings in the even positions. Forcings imputted are: Water temperature [Celsius degrees] and feeding rate [g/individual x d] |
saves .nc; .csv and .asc outputs in the 'Outputs' folder
Postprocess the Mussel spatialized model results
Bass_spatial_post(userpath, output, times, Dates, CS)Bass_spatial_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Bass |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Bass bioenergetic spatialized model preprocessor
Bass_spatial_pre(userpath, forcings)Bass_spatial_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
a list containing the data used by the main script
Bass bioenergetic spatialized model preprocessor - used inside spatialization loop
Bass_spatial_pre_int(userpath, forcings)Bass_spatial_pre_int(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
a list containing data used by the main script
Solves the Seabass bioenergetic balance with a 4th order Runge Kutta method - used in spatialized model
Bass_spatial_RKsolver(Param, Temperature, G, Food, IC, times)Bass_spatial_RKsolver(Param, Temperature, G, Food, IC, times)
Param |
vector containing all metabolic parameters |
Temperature |
water temperature forcing time series |
G |
food entering the cage time series |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
IC |
initial conditions |
times |
vector containing integration extremes and integration timestep |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Creates the folders structure for Bass spatialized model
Bass_spatial_skeleton(userpath)Bass_spatial_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Seabream individual bioenergetic model and performs the interpolation
Bream_ind_dataloader(userpath)Bream_ind_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Seabream bioenergetic individual model differential equations
Bream_ind_equations(Param, Temp, G, Food, weight)Bream_ind_equations(Param, Temp, G, Food, weight)
Param |
vector containing all metabolic parameters |
Temp |
water temperature forcing at time t |
G |
food entering the cage at time t |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
weight |
individual weight at time t |
model output at time t
Seabream bioenergetic individual model
Bream_ind_main(userpath, forcings)Bream_ind_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d] |
A list containing model outputs: weight, excreted quantities and quantities to waste, actual and potential ingestion, temperature limitation functions and metabolic rates
Postprocess the Seabream indivual bioenergetic model results
Bream_ind_post(userpath, output, times, Dates, CS)Bream_ind_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Seabream |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Preprocesses the data for the bioenergetic balance for Sea Bream
Bream_ind_pre(userpath, forcings)Bream_ind_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Solves the Seabream individual bioenergetic balance with a 4th order Runge Kutta method
Bream_ind_RKsolver(Param, Temperature, G, Food, IC, times)Bream_ind_RKsolver(Param, Temperature, G, Food, IC, times)
Param |
vector containing all metabolic parameters |
Temperature |
water temperature forcing time series |
G |
food entering the cage time series |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
IC |
vector containing initial conditions on weight |
times |
vector containing integration extremes and timestep |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Creates the folders structure for Seabream individual bioenergetic model
Bream_ind_skeleton(userpath)Bream_ind_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Seabream population model and performs the interpolation
Bream_pop_dataloader(userpath)Bream_pop_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Seabream bioenergetic population model differential equations
Bream_pop_equations(Param, N, Temp, G, Food, weight)Bream_pop_equations(Param, N, Temp, G, Food, weight)
Param |
vector containing all metabolic parameters |
N |
the number of individuals at time t |
Temp |
water temperature forcing at time t |
G |
food entering the cage at time t |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
weight |
individual weight at time t |
model output at time t
Function that runs the Monte Carlo simulation for the Seabream population model
Bream_pop_loop(Param, Tint, Gint, Food, IC, times, N, userpath)Bream_pop_loop(Param, Tint, Gint, Food, IC, times, N, userpath)
Param |
a vector containing model parameters |
Tint |
the interpolated water temperature time series |
Gint |
the interpolated feeding rate time series |
Food |
the food characterization |
IC |
initial condition |
times |
integration extremes and integration timestep |
N |
time series with number of individuals |
userpath |
the path where the working folder is located |
a list with RK solver outputs
Seabream bioenergetic population model
Bream_pop_main(userpath, forcings)Bream_pop_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d] |
A list containing model outputs: weight, excreted quantities and quantities to waste, actual and potential ingestion, temperature limitation functions and metabolic rates
Postprocess the Bream population bioenergetic model results
Bream_pop_post(userpath, output, times, Dates, N, CS)Bream_pop_post(userpath, output, times, Dates, N, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
N |
the number of individuals |
CS |
the commercial size of Seabream |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Preprocesses the data for the bioenergetic balance for Sea Bream
Bream_pop_pre(userpath, forcings)Bream_pop_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Solves the Seabream population bioenergetic balance with a 4th order Runge Kutta method
Bream_pop_RKsolver(Param, Temperature, G, Food, IC, times, N)Bream_pop_RKsolver(Param, Temperature, G, Food, IC, times, N)
Param |
vector containing all metabolic parameters |
Temperature |
water temperature forcing time series |
G |
food entering the cage time series |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
IC |
initial condition on weight |
times |
integration times |
N |
number of individuals time series |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Creates the folders structure for Seabream population model
Bream_pop_skeleton(userpath)Bream_pop_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Bream spatialized model and performs the interpolation
Bream_spatial_dataloader(userpath)Bream_spatial_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees] and feeding rate [g/individual x d]
Solves the bioenergetic balance for Bream
Bream_spatial_loop(userpath, forcings)Bream_spatial_loop(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
A list containing model outputs: weight, excreted quantities and quantities to waste, actual and potential ingestion, temperature limitation functions and metabolic rates
Solves the bioenergetic balance for Bream
Bream_spatial_main(userpath, forcings)Bream_spatial_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
list containing the time series in the odd positions and realted forcings in the even positions. Forcings imputted are: Water temperature [Celsius degrees] and feeding rate [g/individual x d] |
saves .nc; .csv and .asc outputs in the 'Outputs' folder
Postprocess the Bream spatialized model results
Bream_spatial_post(userpath, output, times, Dates, CS)Bream_spatial_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Bream |
a list containing the model outputs saved by the main script to .nc; .csv and .asc files
Bream bioenergetic spatialized model preprocessor
Bream_spatial_pre(userpath, forcings)Bream_spatial_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
a list containing the data used in the main script
Bream bioenergetic spatialized model preprocessor - used inside spatialization loop
Bream_spatial_pre_int(userpath, forcings)Bream_spatial_pre_int(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
a list containing the data used by the main script
Solves the Seabream bioenergetic balance with a 4th order Runge Kutta method - used in spatialized model
Bream_spatial_RKsolver(Param, Temperature, G, Food, IC, times)Bream_spatial_RKsolver(Param, Temperature, G, Food, IC, times)
Param |
vector containing all metabolic parameters |
Temperature |
water temperature forcing time series |
G |
food entering the cage time series |
Food |
food characterization (Proteins, Lipids, Carbohydrates) |
IC |
initial conditions |
times |
vector containing integration extremes and integration timestep |
a list containing the fish weight, proteines, lipids and carbohydrates wasted or produced with excretions, potential and actual ingestion rates, temperature limitation functions and metabolic rates
Creates the folders structure for Bream spatialized model
Bream_spatial_skeleton(userpath)Bream_spatial_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Clam individual bioenergetic model and performs the interpolation
Clam_ind_dataloader(userpath)Clam_ind_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l], particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Clam bioenergetic individual model differential equations
Clam_ind_equations(Param, Tint, Phy, DT, POCint, POMint, TSSint, Wd)Clam_ind_equations(Param, Tint, Phy, DT, POCint, POMint, TSSint, Wd)
Param |
a vector containing model parameters |
Tint |
the interpolated water temperature at time t |
Phy |
the interpolated phytoplankton at time t |
DT |
the interpolated detritus at time t |
POCint |
the interpolated POC at time t |
POMint |
the interpolated POM at time t |
TSSint |
the interpolated TSS at time t |
Wd |
the weight of the clam at time t |
a list containing the clam weights, temperature limitation functions and metabolic rates at time t
Clam bioenergetic individual model
Clam_ind_main(userpath, forcings)Clam_ind_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l], particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam individual bioenergetic model results
Clam_ind_post(userpath, output, times, Dates, CS)Clam_ind_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Clam |
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic individual model preprocessor
Clam_ind_pre(userpath, forcings)Clam_ind_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l], particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Solves the Clam individual bioenergetic balance with a 4th order Runge Kutta method
clam_ind_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, POMint, TSSint )clam_ind_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, POMint, TSSint )
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Phyint |
the interpolated phytoplankton time series |
DTint |
the interpolated detritus time series |
POCint |
the interpolated POC time series |
POMint |
the interpolated POM time series |
TSSint |
the interpolated TSS time series |
a list containing the clam weights, temperature limitation functions and metabolic rates
Creates the folders structure for Clam individual bioenergetic model
Clam_ind_skeleton(userpath)Clam_ind_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Clam population model and performs the interpolation
Clam_pop_dataloader(userpath)Clam_pop_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l], particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Clam bioenergetic population model differential equations
Clam_pop_equations(Param, Tint, Phy, DT, POCint, POMint, TSSint, Wd)Clam_pop_equations(Param, Tint, Phy, DT, POCint, POMint, TSSint, Wd)
Param |
a vector containing model parameters |
Tint |
the interpolated water temperature at time t |
Phy |
the interpolated phytoplankton at time t |
DT |
the interpolated detritus at time t |
POCint |
the interpolated POC at time t |
POMint |
the interpolated POM at time t |
TSSint |
the interpolated TSS at time t |
Wd |
the weight of the clam at time t |
a list containing the clam weights, temperature limitation functions and metabolic rates at time t
Function that runs the Monte Carlo simulation for the Clam population model
Clam_pop_loop( Param, times, IC, Tint, Phyint, DTint, POCint, POMint, TSSint, N, userpath )Clam_pop_loop( Param, times, IC, Tint, Phyint, DTint, POCint, POMint, TSSint, N, userpath )
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Phyint |
the interpolated phytoplankton time series |
DTint |
the interpolated detritus time series |
POCint |
the interpolated POC time series |
POMint |
the interpolated POM time series |
TSSint |
the interpolated TSS time series |
N |
time series with number of individuals |
userpath |
the path where the working folder is located |
a list with RK solver outputs
Clam bioenergetic population model
Clam_pop_main(userpath, forcings)Clam_pop_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l], particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam population bioenergetic model results
Clam_pop_post(userpath, output, times, Dates, N, CS)Clam_pop_post(userpath, output, times, Dates, N, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
N |
the number of individuals |
CS |
the commercial size of Clam |
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic population model preprocessor
Clam_pop_pre(userpath, forcings)Clam_pop_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l], particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Solves the Clam bioenergetic balance for population with a 4th order Runge Kutta method
Clam_pop_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, POMint, TSSint )Clam_pop_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, POMint, TSSint )
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Phyint |
the interpolated phytoplankton time series |
DTint |
the interpolated detritus time series |
POCint |
the interpolated POC time series |
POMint |
the interpolated POM time series |
TSSint |
the interpolated TSS time series |
a list containing the clam weights, temperature limitation functions and metabolic rates
Creates the folders structure for Clam population model
Clam_pop_skeleton(userpath)Clam_pop_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Clam individual bioenergetic model (alternative version) and performs the interpolation
ClamF_ind_dataloader(userpath)ClamF_ind_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3]
Clam bioenergetic individual model differential equations (alternative version)
ClamF_ind_equations(Param, Tint, Chlint, Ww)ClamF_ind_equations(Param, Tint, Chlint, Ww)
Param |
a vector containing model parameters |
Tint |
the interpolated water temperature at time t |
Chlint |
the interpolated chlorophyll at time t |
Ww |
clam wet weight at time t |
a list containing the clam weights, temperature limitation functions and metabolic rates at time t
Clam bioenergetic individual model (alternative version)
ClamF_ind_main(userpath, forcings)ClamF_ind_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3] |
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam indivual bioenergetic model (alternative version) results
ClamF_ind_post(userpath, output, times, Dates, CS)ClamF_ind_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Clam |
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic individual model preprocessor (alternativer version)
ClamF_ind_pre(userpath, forcings)ClamF_ind_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3]
Solves the Clam bioenergetic balance (alternative version) with a 4th order Runge Kutta method
ClamF_ind_RKsolver(Param, times, IC, Tint, Chlint)ClamF_ind_RKsolver(Param, times, IC, Tint, Chlint)
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Chlint |
the interpolated chlorophyll a time series |
a list containing the clam weights, temperature limitation functions and metabolic rates
Creates the folders structure for Clam individual bioenergetic model (alternative version)
ClamF_ind_skeleton(userpath)ClamF_ind_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Clam population model (alternative version) and performs the interpolation
ClamF_pop_dataloader(userpath)ClamF_pop_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3]
Clam bioenergetic population model differential equations (alternative version)
ClamF_pop_equations(Param, Tint, Chlint, Ww)ClamF_pop_equations(Param, Tint, Chlint, Ww)
Param |
a vector containing model parameters |
Tint |
the interpolated water temperature at time t |
Chlint |
the interpolated chlorophyll at time t |
Ww |
clam wet weight at time t |
a list containing the clam weights, temperature limitation functions and metabolic rates at time t
Function that runs the Monte Carlo simulation for the Clam population model (alternative version)
ClamF_pop_loop(Param, times, IC, Tint, Chlint, N, userpath)ClamF_pop_loop(Param, times, IC, Tint, Chlint, N, userpath)
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Chlint |
the interpolated chlorophyll a time series |
N |
time series with number of individuals |
userpath |
the path where the working folder is located |
a list with RK solver outputs
Clam bioenergetic population model (alternative version)
ClamF_pop_main(userpath, forcings)ClamF_pop_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3] |
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam population bioenergetic model results (alternative model)
ClamF_pop_post(userpath, output, times, Dates, N, CS)ClamF_pop_post(userpath, output, times, Dates, N, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
N |
the number of individuals |
CS |
the commercial size of Clam |
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic population model (alternative version) preprocessor
ClamF_pop_pre(userpath, forcings)ClamF_pop_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3]
Solves the Clam bioenergetic balance (alternative version) with a 4th order Runge Kutta method
ClamF_pop_RKsolver(Param, times, IC, Tint, Chlint)ClamF_pop_RKsolver(Param, times, IC, Tint, Chlint)
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition on weight |
Tint |
the interpolated water temperature time series |
Chlint |
the interpolated chlorophyll a time series |
a list containing the clam weights, temperature limitation functions and metabolic rates
Creates the folders structure for Clam population model (alternative version)
ClamF_pop_skeleton(userpath)ClamF_pop_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Mussel individual bioenergetic model and performs the interpolation
Mussel_ind_dataloader(userpath)Mussel_ind_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Mussel bioenergetic individual model differential equations
Mussel_ind_equations( Param, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, Wb, R, t, trip )Mussel_ind_equations( Param, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, Wb, R, t, trip )
Param |
a vector containing model parameters |
Tint |
the interpolated water temperature at time t |
Phyint |
the interpolated phytoplankton at time t |
DTint |
the interpolated detritus at time t |
POCint |
the interpolated POC at time t |
Ccont |
the C/C content of the POC at time t |
Ncont |
the N/C content of POC at time t |
Pcont |
the P/C content of POC at time t |
POMint |
the interpolated POM at time t |
TSSint |
the interpolated TSS at time t |
Wb |
the somatic tissue dry weight at time t |
R |
the gondadic tissue dry weight at time t |
t |
the time |
trip |
vector containing the flags with resting periods |
the outputs at time t
Solves the bioenergetic balance for Mussel
Mussel_ind_main(userpath, forcings)Mussel_ind_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
A list containing model outputs: weight, length mussel CNP, pseudofaeces CNP production, faeces CNP production, temperature limitation functions, metabolic rates and oxygen consumption
Postprocess the Mussel indivual bioenergetic model results
Mussel_ind_post(userpath, output, times, Dates, CS)Mussel_ind_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Mussel |
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Mussel bioenergetic individual model preprocessor
Mussel_ind_pre(userpath, forcings)Mussel_ind_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Solves the Mussel individual bioenergetic balance with a 4th order Runge Kutta method
Mussel_ind_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint )Mussel_ind_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint )
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Phyint |
the interpolated phytoplankton time series |
DTint |
the interpolated detritus time series |
POCint |
the interpolated POC time series |
Ccont |
the C/C content of the POC |
Ncont |
the N/C content of POC |
Pcont |
the P/C content of POC |
POMint |
the interpolated POM time series |
TSSint |
the interpolated TSS time series |
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Creates the folders structure for Mussel individual bioenergetic model
Mussel_ind_skeleton(userpath)Mussel_ind_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Mussel population model and performs the interpolation
Mussel_pop_dataloader(userpath)Mussel_pop_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Mussel bioenergetic population model differential equations
Mussel_pop_equations( Param, N, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, Wb, R, t, trip )Mussel_pop_equations( Param, N, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, Wb, R, t, trip )
Param |
a vector containing model parameters |
N |
the number of individuals at time t |
Tint |
the interpolated water temperature at time t |
Phyint |
the interpolated phytoplankton at time t |
DTint |
the interpolated detritus at time t |
POCint |
the interpolated POC at time t |
Ccont |
the C/C content of the POC at time t |
Ncont |
the N/C content of POC at time t |
Pcont |
the P/C content of POC at time t |
POMint |
the interpolated POM at time t |
TSSint |
the interpolated TSS at time t |
Wb |
the somatic tissue dry weight at time t |
R |
the gondadic tissue dry weight at time t |
t |
the time |
trip |
vector containing the flags with resting periods |
the outputs at time t
Function that runs the Monte Carlo simulation for the Mussel population model
Mussel_pop_loop( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, N, userpath )Mussel_pop_loop( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, N, userpath )
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Phyint |
the interpolated phytoplankton time series |
DTint |
the interpolated detritus time series |
POCint |
the interpolated POC time series |
Ccont |
the C/C content of the POC |
Ncont |
the N/C content of POC |
Pcont |
the P/C content of POC |
POMint |
the interpolated POM time series |
TSSint |
the interpolated TSS time series |
N |
time series with number of individuals |
userpath |
the path where the working folder is located |
a list with RK solver outputs
Solves the bioenergetic balance for Mussel and simulates a population
Mussel_pop_main(userpath, forcings)Mussel_pop_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
A list containing model outputs: weight, length mussel CNP, pseudofecies CNP production, temperature limitation functions, metabolic rates and oxygen consumption
Postprocess the Mussel population bioenergetic model results
Mussel_pop_post(userpath, output, times, Dates, N, CS)Mussel_pop_post(userpath, output, times, Dates, N, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
N |
the number of individuals |
CS |
the commercial size of Seabass |
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Mussel bioenergetic population model preprocessor
Mussel_pop_pre(userpath, forcings)Mussel_pop_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Solves the Mussel population bioenergetic balance with a 4th order Runge Kutta method
Mussel_pop_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, N )Mussel_pop_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint, N )
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Phyint |
the interpolated phytoplankton time series |
DTint |
the interpolated detritus time series |
POCint |
the interpolated POC time series |
Ccont |
the C/C content of the POC |
Ncont |
the N/C content of POC |
Pcont |
the P/C content of POC |
POMint |
the interpolated POM time series |
TSSint |
the interpolated TSS time series |
N |
the number of indivduals time series |
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Creates the folders structure for Mussel population model
Mussel_pop_skeleton(userpath)Mussel_pop_skeleton(userpath)
userpath |
the path where forcing are located |
Function that loads forcings data for Mussel spatialized model and performs the interpolation
Mussel_spatial_dataloader(userpath)Mussel_spatial_dataloader(userpath)
userpath |
the path where folder containing model inputs and outputs is located |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Solves the bioenergetic balance for Mussel
Mussel_spatial_loop(userpath, forcings)Mussel_spatial_loop(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
A list containing model outputs that main script saves to .nc; .csv and .asc files
Solves the bioenergetic balance for Mussel
Mussel_spatial_main(userpath, forcings)Mussel_spatial_main(userpath, forcings)
userpath |
the path where the working folder is located |
forcings |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l] |
saves .nc; .csv and .asc outputs in the 'Outputs' folder
Postprocess the Mussel spatialized model results
Mussel_spatial_post(userpath, output, times, Dates, CS)Mussel_spatial_post(userpath, output, times, Dates, CS)
userpath |
the path where the working folder is located |
output |
output list containing the output of the RK solver |
times |
the vector containing informations on integration extremes |
Dates |
the vector containing the date |
CS |
the commercial size of Mussel |
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Mussel bioenergetic spatialized model preprocessor
Mussel_spatial_pre(userpath, forcings)Mussel_spatial_pre(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Mussel bioenergetic spatialized model preprocessor - used inside spatialization loop
Mussel_spatial_pre_int(userpath, forcings)Mussel_spatial_pre_int(userpath, forcings)
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
a list containing the time series in the odd positions and realted forcings in the even positions. Forcings returned are: Water temperature [Celsius degrees], Chlorophyll a concentration [mgChl-a/m^3], particulated organic carbon (POC) concentration [mgC/l] and its characterization in terms of C/P and N/P molar ratios, particulated organic matter (POM) concentration [mgC/l], total suspended solids (TSS) concentration [mg/l]
Solves the Mussel individual bioenergetic balance with a 4th order Runge Kutta method for spatialized model
Mussel_spatial_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint )Mussel_spatial_RKsolver( Param, times, IC, Tint, Phyint, DTint, POCint, Ccont, Ncont, Pcont, POMint, TSSint )
Param |
a vector containing model parameters |
times |
integration extremes and integration timestep |
IC |
initial condition |
Tint |
the interpolated water temperature time series |
Phyint |
the interpolated phytoplankton time series |
DTint |
the interpolated detritus time series |
POCint |
the interpolated POC time series |
Ccont |
the C/C content of the POC |
Ncont |
the N/C content of POC |
Pcont |
the P/C content of POC |
POMint |
the interpolated POM time series |
TSSint |
the interpolated TSS time series |
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Creates the folders structure for Mussel spatialized model
Mussel_spatial_skeleton(userpath)Mussel_spatial_skeleton(userpath)
userpath |
the path where forcing are located |
Function that solves the population dynamics equations including discontinuities
Pop_fun(Nseed, mort, manag, times)Pop_fun(Nseed, mort, manag, times)
Nseed |
number of seeded individuals |
mort |
mortality rate |
manag |
list of management actions (seeded/harvested individuals) |
times |
vector containing informations on integration times |
a time series with the number of individuals