FishMet(1) Manual Page

default program interface type, graphical true or command line false.

Output destination (usually directory): all plot and output data files will be saved there. The default value is if this variable is absent or directory is not writeable is the current directory. This parameter affects the program behaviour only in the command line user interface and not in the graphical user interface. Note that fish object data save fish_object_data is saved exactly into the fish_object_file because this is non-human readable internal binary data not intended as the model output. The destination can refer to destination directory or output file name prefix. In the former case it should terminate with the operating system specific directory delimiter (e.g. / on GNU/Linux or \ on Microsoft Windows). If the value of output_dest does not terminate this way, it will refer to the file prefix. It is important that the output destination can also be set with the FFA_MODEL_OUTPUT_DEST environment variable, which takes priority over this configuration file parameter. The following outputs are saved to the output_dest:

Scale units for the time-based plots 1=sec, 2=min, 3=hours.

Default time unit scale for calculating rates. Rate unit is set as digit: 1=s-1, 2=min-1, 3=h-1.

define whether to use the raw absolute or relative for some of the time-based plots, e.g. stomach and midgut mass dynamics. true means relative scales, i.e. stomach or midgut food mass plot displays filling relative to the total capacity, false means that absolute food mass is used.

default discretization interval in minutes that is used to calculate rate, e.g. this interval is used to plot the ingestion rate

default page size (height, width) for the GUI plot window in pixels.

default width of the plot output area in pixels.

default aspect ratio (height/width) of the plot output area.

defines the configuration version tag that is added to all automatically generated output files. The tag should be defined using Subversion "$Revision: 1234 $" keyword. It is then parsed to exclude everything except the revision number, adding "conf_r" prefix. (so configuration_version = "$Revision: 1234 $" translates to "conf_r1234". Note that this behaviour is enabled if the environment variable FFA_MODEL_OUTPUT_TAG_CONFIG_REV is set to any value and disabled otherwise.

This variable defines the file name that contains the food provision scheduling. This file should be in CSV format or a single-column plain text. In a multi-column CSV file, the last column is assumed to contain the feed scheduling. Scheduling is encoded by zero and non-zero values by minute (or by second if food_provisioning_file_by_s is set to TRUE). Here any non-zero value means that food is provided during the respective minute interval, zero means that food is not provided. The file is intended to describe the temporal pattern for 24 h, any longer sequence is discarded. All missing values used for filling the remaining minutes to complete the 24 h are zeroes, i.e. food not provided. The pattern is then propagated for all 24 h periods if food_provision_file_repeat is TRUE or applied once if food_provision_file_repeat is FALSE. Note that the file takes priority over the food ononing pattern defined in food_provision_pattern. Example: food_provision_file_name = "../file_name.csv"

A logical flag that defines if the feed scheduling pattern defined by the food_provision_file_name file will propagate to all 24 h periods or applied just once to the first such period. The default value is TRUE.
Example: food_provision_file_repeat = TRUE

Global logical flag that defines if the feed scheduling pattern defined by the food_provision_file_name file represents the data for each time step (s) (if TRUE) or by minute (FALSE). The default value is FALSE i.e. data are given for each minute.
Example: food_provisioning_file_by_s = FALSE

The name of the CSV file to save general output statistics for specific run of the model.
The default name is "fishmet_stats.csv"
Example: stats_output_file = "data.csv".

This is a logical parameter that defines if the output stats are saved using the long or short format. In the first case, both the input parameters and the output stats are saved/appended into the CSV file. Note that the default value is TRUE.
Example: stats_output_long = TRUE

This parameter define if the prediction timestamp is produced in the output stats file. This timestamp then takes the model execution timestamp and adds the time equivalent to the run_model_hours simulation duration. The default value is FALSE. All timestamps are produced in the following format: 2023/07/21 03:09:50.
Example: stats_output_prediction_stamp = TRUE

The name of the binary file to save the fish object data, i.e. all data for the model fish allowing to resume simulation from a specific fish state (stomach and midgut content, appetite level etc). The default file name is fishmet_fish_state.bin. Note that the file name must have the .bin file extension, otherwise it is not accepted.
Example: fish_object_file = "persistent_data_1.bin"

The name of the CSV data file that defines the stomach emptying parameter matrix, an interpolation grid matrix that defines how long does it take to process full stomach calacity of the feed until no feed remains in the stomach. The matrix defined in this file determines stomach emptying time for a range of fish body mass (columns) and ambient temperatures (rows).

Total number of hours for which the simulation is run. It translates into the raw time steps internally as T = H x 3600, where T is the number of time steps, H is the run_model_hours parameter and 3600 is seconds per hour. Example: run_model_hours = 24.

Default daytime duration, hours. The night time duration is defined as 24-daytime_hours. Note that feeding activity occurs only during the day time and not at night. Example: daytime_hours = 12.

Default hour at which the daytime is normally started. It is also the initial offset for day at the start of the simulation. Example: day_starts_hour = 6.

Ambient temperature ºC. Example: temperature = 14.

Fish body mass at the start of the simulation, g. Example: body_mass = 10.0.

Override body_mass value from fish object file (see fish_object_file) with input parameter value.

Baseline locomotor activity, swimming speed SL/s, during the day as defined by daytime_hours parameter. + Example: baseline_activity_day = 2.5.

Baseline locomotor activity, swimming speed, SL/s, during the day as defined by daytime_hours parameter. + Example: baseline_activity_night = 0.5.

fish stomach mass, max. filling capacity, g. Example: stomach_capacity = 5.0.

fish midgut mass, max. filling capacity, g. Example: midgut_capacity = 10.0.

logical flag determining, when TRUE, that stomach_capacity and midgut_capacity are continuously automatically recalculated based on the body mass body_mass. Note that this can override any fixed parameter values set by the parameter values stomach_capacity and midgut_capacity.
Example: stomach_midgut_automatic = True

Absorption ratio in the midgut, relative to the initial mass of food. Example: absorption_ratio = 0.7.

Delay after ingestion, min. Water uptake occurs during the delay. Example: ingestion_delay = 30.

Proportion of water uptake, relative to the initial food item mass. Example: water_uptake = 0.20.

Water uptake pattern over time is defined by the logistic equation $\frac{ c }{ 1+a e^{-r^2 t} }$, where c is the upper limit of the mass, a and r are logistic parameters and e is natural logarithm base. The a and r parameters of the equation refer to the water_uptake_a and water_uptake_r parameters. See also water_uptake_r. Example: water_uptake_a = 200.0.

Water uptake pattern over time is defined by the logistic equation $\frac{ c }{ 1+a e^{-r^2 t} }$, where c is the upper limit of the mass, a and r are logistic parameters and %e is natural logarithm base. The a and r parameters of the equation refer to the water_uptake_a and water_uptake_r parameters. See also water_uptake_a. Example: water_uptake_r = 0.01.

Delay of digestion, min. This refers to the time interval from the moment the food item gets into the mid-gut until absorption of the food starts. Example: digestion_delay = 20.

The maximum duration a food item can be processed in the fish midgut, min. If it stays in the mid-gut for any longer time, it is evacuated. Example: midgut_maxdur = 180.

Grid array defining the food transport pattern in the stomach. This array defines the time grid for interpolation. Note that normally it takes several hours until the food item fully disappears from stomach (gastric emptying time). This parameter can be set either in hours (small numbers) or in raw seconds (large numbers) and the correct time unit is normally autodetected by the program. See also transport_pattern_r.
Example (s): transport_pattern_t = 0 3000 15000 21600
Example (hours): transport_pattern_t = 0, 0.8, 4, 6

Grid array defining the food transport pattern in the stomach. This array defines the proportion of food mass left in stomach at each level of transport_pattern_t array. See also transport_pattern_t.
Example: transport_pattern_r = 1.0 0.6 0.01 0.0.

Fish appetite at night. This value is normally low because the fish do not feed at night. If the value is absent or negative, fish appetite does not reduce at night.
Example: appetite_night = 0.1

Appetite factor is defined by the logistic equation: $\frac{ c }{ 1+a e^{-r^2 t} }$. This parameter refers to a. See also appetite_factor_r. Example: appetite_factor_a = 50000.0.

Appetite factor is defined by the logistic equation: $\frac{ c }{ 1+a e^{-r^2 t} }$. This parameter refers to r. See also appetite_factor_a. Example: appetite_factor_r = 20.0.

Protective appetite threshold for stomach: this is the maximum value of the stomach appetite signam when the overall fish appetite level depends only on stomach filling. Setting a sufficiently low value provides a way to protect stomach from overfilling.
Example: appetite_threshold_stomach = 0.2

Logistic appetite parameter describing defining the energy appetite component dependence on the energy budget.
Example: appetite_energy_rate = 40.0

Logistic appetite parameter describing defining the energy appetite component dependence on the energy budget.
Example: appetite_energy_shift = 0.2

Activity appetite factor determining how fish locomotor activity increases with increasing appetite.
Example: activity_appetite_factor = 0.5

This is an array of time points that define intervention of stress. The array can be defined either in raw s time scale or in minutes depending on stress_is_min parameter. Example: stress = c(1200, 6000).

The maximum value of the metabolic cost of stress in units of resting metabolic rate (SMR). The actual metabolic cost at each time step scales depending on the time since stress intervention defined by stress array, following the stress pattern described by the stress_grid_hour and stress_grid_fact arrays.
Example: stress_metabolic_cost = 0.5

Defines if stress intervention timing is defined in minutes (TRUE) or raw s (FALSE)).
Example: stress_is_min = TRUE

Stress effect interpolation grid array. stress_grid_hour defines the time since the stress intervention occurs. The second array, stress_grid_fact, defines the intensity of the stress effect.
Example: stress_grid_hour = c(0, 10, 20, 40, 50, 72)

Stress effect interpolation grid array. stress_grid_fact defines the intensity of the stress effect. For example, if it is equal to 1.0, appetite is completely suppressed. The other array, stress_grid_hour defines the time scale (h) for each point.
Example: stress_grid_fact = c(1.0, 0.9, 0.7, 0.2, 0.1, 0.0)

Michaelis-Meneten food absorption parameter in midgut, r_max, relative to the mass of the food item. Rate is per second, the basic discrete step of the model. E.g. 0.8 means that 80% of the food item mass can be absorbed at maximum. See also midgut_michaelis_k. Example: midgut_michaelis_r_max = 0.9.

Michaelis-Meneten food absorption parameter in midgut, K_M, relative to the total midgut capacity (e.g. 0.25 means a quarter of the total midgut mass). See also midgut_michaelis_k.
Example: midgut_michaelis_k = 0.25.

Temperature adjustment for absorption is controlled by the two parameters that define the temperature adfjustment grid factor for the Michaelis-Menten equation: midgut_temp_fact_t and midgut_temp_fact_m. This parameter is the temperature grid for Michaelis-Menten absorption process.
Example: midgut_temp_fact_t = c(5.0, 10.0, 15.0, 25.0).

Temperature adjustment for absorption is controlled by the two parameters that define the temperature adfjustment grid factor for the Michaelis-Menten equation: midgut_temp_fact_t and midgut_temp_fact_m. This parameter is the temperature grid for Michaelis-Menten absorption process. This is the speedup factor grid for the Michaelis-Menten absorption process for the temperatures defined by midgut_temp_fact_t.
Example: midgut_temp_fact_m = c(0.4, 0.6, 1.0, 8.0)

Interpolation X axis grid defining the SMR function on the temperature ºC.

Interpolation grid Y axis defining the SMR function on the temperature. SMR unit is $mg \; O_{2} \; kg^{-1} \; h^{-1}$.

A parameter defining branchial and urine (ZE+6UE) energy consumption as a factor to SMR, e.g. 0.3 means (UE+ZE) = 0.3*SMR. This is an alternative to branchial_ammonia_rate. If both branchial_energy_factor and branchial_ammonia_rate are defined, the former parameter always takes priority.
Example: branchial_energy_factor = 0.1

A parameter defining branchial and urine (ZE+6UE) energy consumption as a fixed ammonia excretion rate, micro-mol per g body mass per hour. This is an alternative to branchial_energy_factor. If both branchial_energy_factor and branchial_ammonia_rate are defined, the former parameter always takes priority.
Example: branchial_ammonia_rate = 0.25

Defines the specific dynamic action (SDA) that depends on the absorption rate. There are two parameters that define the linear relationship between absorption rate and SDA increase. This parameter defines the maximum absorption rate when the maximum SDA (defined by sda_energy_factor_max is reached.
Example: sda_absorption_rate_max = 0.0007

Defines the specific dynamic action (SDA) that depends on the absorption rate. There are two parameters that define the linear relationship bet ween absorption rate and SDA increase. This parameter defines the maximum SDA reached at the maximum absorption rate defined by sda_absorption_rate_max. For example, this parameter equal to 2.0 means that SDA = SMR * 2.0 at the maximum absorption rate.
Example: sda_energy_factor_max = 2.0

Basic dry mass of one food item (g). Example: food_item_mass = 0.25.

Gross energy content of the feed, MJ/kg (= kJ/g) Example: feed_gross_energy = 23.0.

Rate of food item input, per min. Example: food_input_rate = 6.0.

Food provision patterning is determined by an array defining the time intervals (min) when food is provisioned and not provisioned e.g. a value of 10 230 means 10 min food is given followed by 230 min not given. Note also that any arbitrary food scheduling can be obtained by encoding periods of food provisioning and not provisioning in the food_provision_file_name parameter. Example: food_provision_pattern = 10 230.

The offset (delay, min) to start feeding at the beginning of the 24 hour period. The feeding pattern defined by food provision pattern starts every 24h period after this offset. For example, if the offset is set to 180 min, this means that the first feeding session defined by the food_provision_pattern begins 3h (180 min) after the start of the day. Example: feed_start_offset = 180

The stomach emptying parameter matrix, an interpolation grid matrix that defines how long does it take to process full stomach calacity of the feed until no feed remains in the stomach. The matrix is defined in a file set by stomach_emptying_matrix.

Get brief help on the commands. Several subcommands can be used: parameters, plot.

Run the model with the default parameters. Alternative alias: start.

Reset all model parameters to the default values from the configuration file. Alternative alias: restart.

exit the program.

Set any model parameter defined in Model parameters. Example: set run_model_hours=24. Another use of the set command is to define the output format for saving plots (see save command): set format or set save_format, then define one of the possible output formats: PDF, PNG, SVG, BMP, GIF, EPS, WMF, CGM. This command is also used to define rate interval: set rate_interval as well as to define override flags.

Produce parameter plots or model output plots. To save a plot to a disk file, use the related save command. Rate plots can have different rate interval using set rate_interval command. Example: plot stomach_transport.
Subcommands:

Save a plot defined as in the plot subcommand. This command also requires two additional parameters: plot type as in plot and the file name. Example: save stomach_transport plot_01.pdf.
Another use of this command is for saving model output data (CSV formatted table):

This command is used to print specific model parameters.

Adjust the stomach transport parameter arrays for the body_mass and ambient temperature. See also stomach emptying matrix.

Initiate output of the general model statistics into stats_output_file csv output data file. Note that this results in writing the column headers and the first row of the data. All subsequent data output should use the append statistics command. Warning: The output command will overwrite any existing CSV file, be careful!.

Append general statistics data for the current run of the model. Note that the first output should use the output statistics command.

Execute some operating system specific command. This command can be useful, for example, for checking files from within the model program, moving files, deleting temporary files etc. Example: shell dir /w (this will show all files in the working directory on Windows without size, timestamp and other details).