| Version: | 1.5.5 |
| Title: | R Package for Aqua Culture |
| Maintainer: | Baldan D. <damiano.baldan91@gmail.com> |
| Imports: | matrixStats, rstudioapi, plotrix, raster, sp |
| Encoding: | UTF-8 |
| Suggests: | MASS, knitr, rmarkdown |
| 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. |
| License: | MIT + file LICENSE |
| RoxygenNote: | 7.2.3 |
| VignetteBuilder: | knitr |
| NeedsCompilation: | no |
| Packaged: | 2023-05-02 12:33:41 UTC; Damiano |
| Author: | Baldan D. [aut, cre], Palazzo D. [ctb], Porporato E.M.D [ctb], Brigolin D. [ctb] |
| Repository: | CRAN |
| Date/Publication: | 2023-05-02 13:00:02 UTC |
Solves the Seabass bioenergetic balance with a 4th order Runge Kutta method
Description
Solves the Seabass bioenergetic balance with a 4th order Runge Kutta method
Usage
Bass_ind_RKsolver(Param, Temperature, G, Food, IC, times)
Arguments
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 |
Value
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
Function that loads forcings data for Seabass individual bioenergetic model and performs the interpolation
Description
Function that loads forcings data for Seabass individual bioenergetic model and performs the interpolation
Usage
Bass_ind_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Seabass bioenergetic individual model differential equations
Usage
Bass_ind_equations(Param, Temp, G, Food, weight)
Arguments
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 |
Value
model output at time t
Seabass bioenergetic individual model
Description
Solves the bioenergetic balance for Seabass
Usage
Bass_ind_main(userpath, forcings)
Arguments
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] |
Value
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
Description
Seabass bioenergetic individual model postprocessor
Usage
Bass_ind_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
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
Description
Seabass bioenergetic individual model preprocessor
Usage
Bass_ind_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Seabass individual bioenergetic model
Description
Creates the folders structure for Seabass individual bioenergetic model
Usage
Bass_ind_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Seabass population bioenergetic balance with a 4th order Runge Kutta method
Description
Solves the Seabass population bioenergetic balance with a 4th order Runge Kutta method
Usage
Bass_pop_RKsolver(Param, Temperature, G, Food, IC, times, N)
Arguments
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 |
Value
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
Function that loads forcings data for Seabass population model and performs the interpolation
Description
Function that loads forcings data for Seabass population model and performs the interpolation
Usage
Bass_pop_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Seabass bioenergetic population model differential equations
Usage
Bass_pop_equations(Param, N, Temp, G, Food, weight)
Arguments
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 |
Value
model output at time t
Function that runs the Monte Carlo simulation for the Seabass population model
Description
Function that runs the Monte Carlo simulation for the Seabass population model
Usage
Bass_pop_loop(Param, Tint, Gint, Food, IC, times, N, userpath)
Arguments
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 |
Value
a list with RK solver outputs
Seabass bioenergetic population model
Description
Seabass bioenergetic population model
Usage
Bass_pop_main(userpath, forcings)
Arguments
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] |
Value
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
Description
Postprocess the Seabass population bioenergetic model results
Usage
Bass_pop_post(userpath, output, times, Dates, N, CS)
Arguments
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 |
Value
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
Description
Seabass bioenergetic population model preprocessor
Usage
Bass_pop_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Seabass population model
Description
Creates the folders structure for Seabass population model
Usage
Bass_pop_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Seabass bioenergetic balance with a 4th order Runge Kutta method - used in spatialized model
Description
Solves the Seabass bioenergetic balance with a 4th order Runge Kutta method - used in spatialized model
Usage
Bass_spatial_RKsolver(Param, Temperature, G, Food, IC, times)
Arguments
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 |
Value
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
Function that loads forcings data for Bass spatialized model and performs the interpolation
Description
Function that loads forcings data for Bass spatialized model and performs the interpolation
Usage
Bass_spatial_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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]
Bass bioenergetic spatialized model - spatialization loop
Description
Solves the bioenergetic balance for Bass
Usage
Bass_spatial_loop(userpath, forcings)
Arguments
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] |
Value
a list containing the outputs that main script saves to .nc; .csv and .asc files
Bass bioenergetic spatialized model - spatialization loop
Description
Solves the bioenergetic balance for Bass
Usage
Bass_spatial_main(userpath, forcings)
Arguments
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] |
Value
saves .nc; .csv and .asc outputs in the 'Outputs' folder
Postprocess the Mussel spatialized model results
Description
Postprocess the Mussel spatialized model results
Usage
Bass_spatial_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
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
Description
Bass bioenergetic spatialized model preprocessor
Usage
Bass_spatial_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
Value
a list containing the data used by the main script
Bass bioenergetic spatialized model preprocessor - used inside spatialization loop
Description
Bass bioenergetic spatialized model preprocessor - used inside spatialization loop
Usage
Bass_spatial_pre_int(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
Value
a list containing data used by the main script
Creates the folders structure for Bass spatialized model
Description
Creates the folders structure for Bass spatialized model
Usage
Bass_spatial_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Seabream individual bioenergetic balance with a 4th order Runge Kutta method
Description
Solves the Seabream individual bioenergetic balance with a 4th order Runge Kutta method
Usage
Bream_ind_RKsolver(Param, Temperature, G, Food, IC, times)
Arguments
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 |
Value
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
Function that loads forcings data for Seabream individual bioenergetic model and performs the interpolation
Description
Function that loads forcings data for Seabream individual bioenergetic model and performs the interpolation
Usage
Bream_ind_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Seabream bioenergetic individual model differential equations
Usage
Bream_ind_equations(Param, Temp, G, Food, weight)
Arguments
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 |
Value
model output at time t
Seabream bioenergetic individual model
Description
Seabream bioenergetic individual model
Usage
Bream_ind_main(userpath, forcings)
Arguments
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] |
Value
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
Description
Postprocess the Seabream indivual bioenergetic model results
Usage
Bream_ind_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
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
Seabream bioenergetic individual model preprocessor
Description
Preprocesses the data for the bioenergetic balance for Sea Bream
Usage
Bream_ind_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Seabream individual bioenergetic model
Description
Creates the folders structure for Seabream individual bioenergetic model
Usage
Bream_ind_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Seabream population bioenergetic balance with a 4th order Runge Kutta method
Description
Solves the Seabream population bioenergetic balance with a 4th order Runge Kutta method
Usage
Bream_pop_RKsolver(Param, Temperature, G, Food, IC, times, N)
Arguments
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 |
Value
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
Function that loads forcings data for Seabream population model and performs the interpolation
Description
Function that loads forcings data for Seabream population model and performs the interpolation
Usage
Bream_pop_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Seabream bioenergetic population model differential equations
Usage
Bream_pop_equations(Param, N, Temp, G, Food, weight)
Arguments
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 |
Value
model output at time t
Function that runs the Monte Carlo simulation for the Seabream population model
Description
Function that runs the Monte Carlo simulation for the Seabream population model
Usage
Bream_pop_loop(Param, Tint, Gint, Food, IC, times, N, userpath)
Arguments
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 |
Value
a list with RK solver outputs
Seabream bioenergetic population model
Description
Seabream bioenergetic population model
Usage
Bream_pop_main(userpath, forcings)
Arguments
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] |
Value
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
Description
Postprocess the Bream population bioenergetic model results
Usage
Bream_pop_post(userpath, output, times, Dates, N, CS)
Arguments
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 |
Value
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
Seabream bioenergetic population model preprocessor
Description
Preprocesses the data for the bioenergetic balance for Sea Bream
Usage
Bream_pop_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Seabream population model
Description
Creates the folders structure for Seabream population model
Usage
Bream_pop_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Seabream bioenergetic balance with a 4th order Runge Kutta method - used in spatialized model
Description
Solves the Seabream bioenergetic balance with a 4th order Runge Kutta method - used in spatialized model
Usage
Bream_spatial_RKsolver(Param, Temperature, G, Food, IC, times)
Arguments
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 |
Value
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
Function that loads forcings data for Bream spatialized model and performs the interpolation
Description
Function that loads forcings data for Bream spatialized model and performs the interpolation
Usage
Bream_spatial_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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]
Bream bioenergetic spatialized model - spatialization loop
Description
Solves the bioenergetic balance for Bream
Usage
Bream_spatial_loop(userpath, forcings)
Arguments
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] |
Value
A list containing model outputs: weight, excreted quantities and quantities to waste, actual and potential ingestion, temperature limitation functions and metabolic rates
Bream bioenergetic spatialized model - spatialization loop
Description
Solves the bioenergetic balance for Bream
Usage
Bream_spatial_main(userpath, forcings)
Arguments
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] |
Value
saves .nc; .csv and .asc outputs in the 'Outputs' folder
Postprocess the Bream spatialized model results
Description
Postprocess the Bream spatialized model results
Usage
Bream_spatial_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
a list containing the model outputs saved by the main script to .nc; .csv and .asc files
Bream bioenergetic spatialized model preprocessor
Description
Bream bioenergetic spatialized model preprocessor
Usage
Bream_spatial_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
Value
a list containing the data used in the main script
Bream bioenergetic spatialized model preprocessor - used inside spatialization loop
Description
Bream bioenergetic spatialized model preprocessor - used inside spatialization loop
Usage
Bream_spatial_pre_int(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
Value
a list containing the data used by the main script
Creates the folders structure for Bream spatialized model
Description
Creates the folders structure for Bream spatialized model
Usage
Bream_spatial_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Clam bioenergetic balance (alternative version) with a 4th order Runge Kutta method
Description
Solves the Clam bioenergetic balance (alternative version) with a 4th order Runge Kutta method
Usage
ClamF_ind_RKsolver(Param, times, IC, Tint, Chlint)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates
Function that loads forcings data for Clam individual bioenergetic model (alternative version) and performs the interpolation
Description
Function that loads forcings data for Clam individual bioenergetic model (alternative version) and performs the interpolation
Usage
ClamF_ind_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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)
Description
Clam bioenergetic individual model differential equations (alternative version)
Usage
ClamF_ind_equations(Param, Tint, Chlint, Ww)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates at time t
Clam bioenergetic individual model (alternative version)
Description
Clam bioenergetic individual model (alternative version)
Usage
ClamF_ind_main(userpath, forcings)
Arguments
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] |
Value
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam indivual bioenergetic model (alternative version) results
Description
Postprocess the Clam indivual bioenergetic model (alternative version) results
Usage
ClamF_ind_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic individual model preprocessor (alternativer version)
Description
Clam bioenergetic individual model preprocessor (alternativer version)
Usage
ClamF_ind_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Clam individual bioenergetic model (alternative version)
Description
Creates the folders structure for Clam individual bioenergetic model (alternative version)
Usage
ClamF_ind_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Clam bioenergetic balance (alternative version) with a 4th order Runge Kutta method
Description
Solves the Clam bioenergetic balance (alternative version) with a 4th order Runge Kutta method
Usage
ClamF_pop_RKsolver(Param, times, IC, Tint, Chlint)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates
Function that loads forcings data for Clam population model (alternative version) and performs the interpolation
Description
Function that loads forcings data for Clam population model (alternative version) and performs the interpolation
Usage
ClamF_pop_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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)
Description
Clam bioenergetic population model differential equations (alternative version)
Usage
ClamF_pop_equations(Param, Tint, Chlint, Ww)
Arguments
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 |
Value
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)
Description
Function that runs the Monte Carlo simulation for the Clam population model (alternative version)
Usage
ClamF_pop_loop(Param, times, IC, Tint, Chlint, N, userpath)
Arguments
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 |
Value
a list with RK solver outputs
Clam bioenergetic population model (alternative version)
Description
Clam bioenergetic population model (alternative version)
Usage
ClamF_pop_main(userpath, forcings)
Arguments
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] |
Value
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam population bioenergetic model results (alternative model)
Description
Postprocess the Clam population bioenergetic model results (alternative model)
Usage
ClamF_pop_post(userpath, output, times, Dates, N, CS)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic population model (alternative version) preprocessor
Description
Clam bioenergetic population model (alternative version) preprocessor
Usage
ClamF_pop_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Clam population model (alternative version)
Description
Creates the folders structure for Clam population model (alternative version)
Usage
ClamF_pop_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Function that loads forcings data for Clam individual bioenergetic model and performs the interpolation
Description
Function that loads forcings data for Clam individual bioenergetic model and performs the interpolation
Usage
Clam_ind_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Clam bioenergetic individual model differential equations
Usage
Clam_ind_equations(Param, Tint, Phy, DT, POCint, POMint, TSSint, Wd)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates at time t
Clam bioenergetic individual model
Description
Clam bioenergetic individual model
Usage
Clam_ind_main(userpath, forcings)
Arguments
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] |
Value
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam individual bioenergetic model results
Description
Postprocess the Clam individual bioenergetic model results
Usage
Clam_ind_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic individual model preprocessor
Description
Clam bioenergetic individual model preprocessor
Usage
Clam_ind_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Clam individual bioenergetic model
Description
Creates the folders structure for Clam individual bioenergetic model
Usage
Clam_ind_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Clam bioenergetic balance for population with a 4th order Runge Kutta method
Description
Solves the Clam bioenergetic balance for population with a 4th order Runge Kutta method
Usage
Clam_pop_RKsolver(
Param,
times,
IC,
Tint,
Phyint,
DTint,
POCint,
POMint,
TSSint
)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates
Function that loads forcings data for Clam population model and performs the interpolation
Description
Function that loads forcings data for Clam population model and performs the interpolation
Usage
Clam_pop_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Clam bioenergetic population model differential equations
Usage
Clam_pop_equations(Param, Tint, Phy, DT, POCint, POMint, TSSint, Wd)
Arguments
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 |
Value
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
Description
Function that runs the Monte Carlo simulation for the Clam population model
Usage
Clam_pop_loop(
Param,
times,
IC,
Tint,
Phyint,
DTint,
POCint,
POMint,
TSSint,
N,
userpath
)
Arguments
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 |
Value
a list with RK solver outputs
Clam bioenergetic population model
Description
Clam bioenergetic population model
Usage
Clam_pop_main(userpath, forcings)
Arguments
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] |
Value
A list containing model outputs: weights, temperature limitation functions and metabolic rates
Postprocess the Clam population bioenergetic model results
Description
Postprocess the Clam population bioenergetic model results
Usage
Clam_pop_post(userpath, output, times, Dates, N, CS)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates
Clam bioenergetic population model preprocessor
Description
Clam bioenergetic population model preprocessor
Usage
Clam_pop_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Clam population model
Description
Creates the folders structure for Clam population model
Usage
Clam_pop_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Mussel individual bioenergetic balance with a 4th order Runge Kutta method
Description
Solves the Mussel individual bioenergetic balance with a 4th order Runge Kutta method
Usage
Mussel_ind_RKsolver(
Param,
times,
IC,
Tint,
Phyint,
DTint,
POCint,
Ccont,
Ncont,
Pcont,
POMint,
TSSint
)
Arguments
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 |
Value
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Function that loads forcings data for Mussel individual bioenergetic model and performs the interpolation
Description
Function that loads forcings data for Mussel individual bioenergetic model and performs the interpolation
Usage
Mussel_ind_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Mussel bioenergetic individual model differential equations
Usage
Mussel_ind_equations(
Param,
Tint,
Phyint,
DTint,
POCint,
Ccont,
Ncont,
Pcont,
POMint,
TSSint,
Wb,
R,
t,
trip
)
Arguments
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 |
Value
the outputs at time t
Mussel bioenergetic individual model
Description
Solves the bioenergetic balance for Mussel
Usage
Mussel_ind_main(userpath, forcings)
Arguments
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] |
Value
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
Description
Postprocess the Mussel indivual bioenergetic model results
Usage
Mussel_ind_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
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
Description
Mussel bioenergetic individual model preprocessor
Usage
Mussel_ind_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing model forcings |
Value
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]
Creates the folders structure for Mussel individual bioenergetic model
Description
Creates the folders structure for Mussel individual bioenergetic model
Usage
Mussel_ind_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Mussel population bioenergetic balance with a 4th order Runge Kutta method
Description
Solves the Mussel population bioenergetic balance with a 4th order Runge Kutta method
Usage
Mussel_pop_RKsolver(
Param,
times,
IC,
Tint,
Phyint,
DTint,
POCint,
Ccont,
Ncont,
Pcont,
POMint,
TSSint,
N
)
Arguments
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 |
Value
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Function that loads forcings data for Mussel population model and performs the interpolation
Description
Function that loads forcings data for Mussel population model and performs the interpolation
Usage
Mussel_pop_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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
Description
Mussel bioenergetic population model differential equations
Usage
Mussel_pop_equations(
Param,
N,
Tint,
Phyint,
DTint,
POCint,
Ccont,
Ncont,
Pcont,
POMint,
TSSint,
Wb,
R,
t,
trip
)
Arguments
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 |
Value
the outputs at time t
Function that runs the Monte Carlo simulation for the Mussel population model
Description
Function that runs the Monte Carlo simulation for the Mussel population model
Usage
Mussel_pop_loop(
Param,
times,
IC,
Tint,
Phyint,
DTint,
POCint,
Ccont,
Ncont,
Pcont,
POMint,
TSSint,
N,
userpath
)
Arguments
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 |
Value
a list with RK solver outputs
Mussel bioenergetic population model
Description
Solves the bioenergetic balance for Mussel and simulates a population
Usage
Mussel_pop_main(userpath, forcings)
Arguments
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] |
Value
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
Description
Postprocess the Mussel population bioenergetic model results
Usage
Mussel_pop_post(userpath, output, times, Dates, N, CS)
Arguments
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 |
Value
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
Description
Mussel bioenergetic population model preprocessor
Usage
Mussel_pop_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
Value
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]
Creates the folders structure for Mussel population model
Description
Creates the folders structure for Mussel population model
Usage
Mussel_pop_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Solves the Mussel individual bioenergetic balance with a 4th order Runge Kutta method for spatialized model
Description
Solves the Mussel individual bioenergetic balance with a 4th order Runge Kutta method for spatialized model
Usage
Mussel_spatial_RKsolver(
Param,
times,
IC,
Tint,
Phyint,
DTint,
POCint,
Ccont,
Ncont,
Pcont,
POMint,
TSSint
)
Arguments
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 |
Value
a list containing the weights of the mussel, the excreted CNP, the mussel CNP, temperature limitation functions, metabolic rates, oxygen consumption
Function that loads forcings data for Mussel spatialized model and performs the interpolation
Description
Function that loads forcings data for Mussel spatialized model and performs the interpolation
Usage
Mussel_spatial_dataloader(userpath)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
Value
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 - spatialization loop
Description
Solves the bioenergetic balance for Mussel
Usage
Mussel_spatial_loop(userpath, forcings)
Arguments
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] |
Value
A list containing model outputs that main script saves to .nc; .csv and .asc files
Mussel bioenergetic spatialized model - spatialization loop
Description
Solves the bioenergetic balance for Mussel
Usage
Mussel_spatial_main(userpath, forcings)
Arguments
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] |
Value
saves .nc; .csv and .asc outputs in the 'Outputs' folder
Postprocess the Mussel spatialized model results
Description
Postprocess the Mussel spatialized model results
Usage
Mussel_spatial_post(userpath, output, times, Dates, CS)
Arguments
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 |
Value
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
Description
Mussel bioenergetic spatialized model preprocessor
Usage
Mussel_spatial_pre(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
Value
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
Description
Mussel bioenergetic spatialized model preprocessor - used inside spatialization loop
Usage
Mussel_spatial_pre_int(userpath, forcings)
Arguments
userpath |
the path where folder containing model inputs and outputs is located |
forcings |
a list containing forcings used by the model |
Value
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]
Creates the folders structure for Mussel spatialized model
Description
Creates the folders structure for Mussel spatialized model
Usage
Mussel_spatial_skeleton(userpath)
Arguments
userpath |
the path where forcing are located |
Function that solves the population dynamics equations including discontinuities
Description
Function that solves the population dynamics equations including discontinuities
Usage
Pop_fun(Nseed, mort, manag, times)
Arguments
Nseed |
number of seeded individuals |
mort |
mortality rate |
manag |
list of management actions (seeded/harvested individuals) |
times |
vector containing informations on integration times |
Value
a time series with the number of individuals
Solves the Clam individual bioenergetic balance with a 4th order Runge Kutta method
Description
Solves the Clam individual bioenergetic balance with a 4th order Runge Kutta method
Usage
clam_ind_RKsolver(
Param,
times,
IC,
Tint,
Phyint,
DTint,
POCint,
POMint,
TSSint
)
Arguments
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 |
Value
a list containing the clam weights, temperature limitation functions and metabolic rates