Package 'LobsterCatch'

This function calculates the probability of entry into a trap, also known as catchability. It includes the parameters described in Addison and Bell (1997), and can also incorporate the length of the catch while calculating the catchability.

Description

This function calculates the probability of entry into a trap, also known as catchability. It includes the parameters described in Addison and Bell (1997), and can also incorporate the length of the catch while calculating the catchability.

Usage

catchability(
  q0,
  qmin,
  saturationThreshold,
  Ct,
  lengthBased,
  lobLengthThreshold,
  lobSize = NA,
  sexBased,
  lobSex
)

Arguments

q0	is the initial probability of entry into an empty trap (range is from 0-1). Default value is 0.5.
qmin	is the asymptotic minimum probability of entry with default value being 0.
saturationThreshold	is the number of lobsters in a trap at which the probability of another lobster entering the trap is zero (i.e. no more entry due to agnostic behavior of trapped lobsters).
Ct	is the number of caught lobster
lengthBased	Logical. If TRUE the length of lobsters caught will be taken into account
lobLengthThreshold	Logical.If TRUE the carapace length (in milliliters) beyond which there is no chance of catching another lobster due to bold agnostic behavior of large lobsters.
lobSize	is a size frequency dataset that is representative of the population and can be incorporated to the model.
sexBased	Logical. If TRUE, lobster sex is taken into account and user must provide a list containing sex distribution for the simulated population
lobSex	is the sex of trapped lobster

Value

Returns the probability of entry to trap.

References

Julian T. Addison and Michael C. Bell (1997), Simulation modelling of capture processes in trap fisheries for clawed lobsters, Marine Freshwater Research, 48(8), 1035-1044, https://www.publish.csiro.au/MF/MF97169

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This function models movement of lobsters toward the trap.The distance of lobsters to trap determines the magnitude of those moves. As lobster gets closer to the trap, the magnitude of its directional move becomes larger and the random move becomes smaller.

Description

This function models movement of lobsters toward the trap.The distance of lobsters to trap determines the magnitude of those moves. As lobster gets closer to the trap, the magnitude of its directional move becomes larger and the random move becomes smaller.

Usage

directionalMove(
  Lobster,
  dStep,
  minDistoTrap,
  Trap,
  radiusOfInfluence,
  currentZoI
)

Arguments

Lobster	location of lobster in the grid in x and y coordinates.
dStep	Distance that each lobster moves during one time step.
minDistoTrap	Distance from the trap.
Trap	location of trap in the arena.
radiusOfInfluence	Radius of influence for the baited trap.
currentZoI	Radius of influence in each time step given the bait shrinkage.

Value

Returns the new coordinates of each lobster in the arena after each directional move.

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This function calculates the variance to mean ratio (also known as dispersion index).

Description

This function calculates the variance to mean ratio (also known as dispersion index).

Usage

dispersion(x)

Arguments

x	is a numeric vector.

Value

Returns the dispersion index.

---

The function finds the closest trap to a lobster and calculates the distance.

Description

The function finds the closest trap to a lobster and calculates the distance.

Usage

distanceToClosestTrap(Lobster, Trap)

Arguments

Lobster	location of lobster in the arena
Trap	location of trap in the arena

Value

Returns distance to closest trap and saves the trap number in case of multiple traps.

---

This function calculates the Euclidean distance between Trap(s) and each lobster. The function is internally called in distanceToClosestTrap function.

Description

This function calculates the Euclidean distance between Trap(s) and each lobster. The function is internally called in distanceToClosestTrap function.

Usage

distanceToTrapCalculator(Lobster, Trap)

Arguments

Lobster	location of lobster in the grid in x and y coordinates.
Trap	location of trap in the grid in x and y coordinates.

Value

Returns the distance to trap.

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This function extracts the results of simulation.

Description

This function extracts the results of simulation.

Usage

GetSimOutput(x, mls = 82.5)

Arguments

x	is an object generated by SimulateLobsterMovement function.
mls	is the minimum legal size(mls) in mm. The default is 82.5 mm.

Value

Returns the followings for each replicate: the number of lobsters caught, legal catch weight (bigger than mls), total catch weight and length of time to reach maximum catch.

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This function simulates an arena (or grid) with lobsters in it based on the provided density, size and sex distribution.

Description

This function simulates an arena (or grid) with lobsters in it based on the provided density, size and sex distribution.

Usage

initialLobsterGrid(
  nrowgrids,
  ncolgrids,
  unitarea,
  initlambda,
  initD,
  lobsterSizeFile,
  lobsterSexDist
)

Arguments

nrowgrids	is a numeric value which defines the number of rows of the arena.
ncolgrids	is a numeric value which defines the number of columns of the arena.
unitarea	is the unit area used for estimating density of lobsters.
initlambda	is the density of lobsters at the beginning of simulation.
initD	is the dispersion index of lobsters on seabed at the beginning of the simulation.
lobsterSizeFile	is a csv file that contains the frequency of lobsters size class.
lobsterSexDist	is a list that contains the sex ratio of lobsters. Possible values are M=male, F=female, MM=mature male, BF=berried female)

Value

Returns x and y coordinates of simulated lobsters at the beginning.

---

Lobster size frequency data

Description

The dataset contains frequency of each size bin (from Carapace length of 50 mm to 200 mm)

Usage

data(LobsterSizeFreqs)

Format

A data frame with 31 rows and 2 variables

Details

• bins (Size groups/bins)

• freq (Frequency)

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The function randomly selects an angle (0:360) and moves the lobster. This function is called when a lobster is outside the area of influence.

Description

The function randomly selects an angle (0:360) and moves the lobster. This function is called when a lobster is outside the area of influence.

Usage

randomMove(Lobster, dStep)

Arguments

Lobster	location of lobster in x and y coordinates
dStep	is how much a lobster moves in each time step

Value

Returns the new coordinates of each lobster

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This function replicates the coordinates where there are multiple lobsters

Description

This function replicates the coordinates where there are multiple lobsters

Usage

replicateCoordinates(d)

Arguments

d	is a data frame containing x and y coordinates of lobsters and number of lobsters at each coordinate

Value

Returns a data frame

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This function generates a Poisson or a negative binomial distribution for lobsters in the arena

Description

This function generates a Poisson or a negative binomial distribution for lobsters in the arena

Usage

rpoisD(n, lambda, D = 1)

Arguments

n	is the number of lobsters to be generated
lambda	is the mean density of lobsters
D	is the dispersion index to be used. Default value is 1

Value

A vector of integers that is used as initial distribution of lobsters

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Function to run the simulation based on defined parameters

Description

Function to run the simulation based on defined parameters

Usage

SimulateLobsterMovement(p)

Arguments

p	is a list of all input variables

Value

Returns a list

See Also

Examples of the input parameters and more details can be found here: https://github.com/pnickchi/lobstercatch/blob/main/Examplecode.R

Examples

p = list()
p$nrowgrids = 10
p$ncolgrids = 10
p$ngrids = p$nrowgrids * p$ncolgrids
p$unitarea = 1
p$initlambda = 0.5
p$dStep = 1
p$howClose = 1
p$initD = 1
p$shrinkage = 0.993
p$currentZoI = 15
p$radiusOfInfluence = 15
p$q0 = 0.5
p$qmin = 0
p$Trap = data.frame( x = c(5), y = c(5) )
p$ntraps = nrow(p$Trap)
p$saturationThreshold = 5
p$lengthBased = FALSE
p$lobsterSizeFile =
'https://raw.githubusercontent.com/vpourfaraj/lobsterCatch/main/inst/extdata/LobsterSizeFreqs.csv'
p$lobLengthThreshold = 115
p$trapSaturation = FALSE
p$sexBased = FALSE
p$lobsterSexDist = list(labels = c('M','F','MM','BF'),
                        prob1 = c(0.55,0.35,0.05,0.05),
                        prob2 = c(0.5,0.50,0,0),
                        lobsterMatThreshold = 100)
p$realizations = 2
p$tSteps = 2
Simrun = SimulateLobsterMovement(p)

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This function determines if lobster gets into a trap and is caught.

Description

This function determines if lobster gets into a trap and is caught.

Usage

trapInPath(loc1, loc2, Trap, howClose)

Arguments

loc1	is the location of lobster at the start of each time step
loc2	is the location of lobster at the end of each time step
Trap	is the location of trap
howClose	The area within which a lobster considered trapped

Value

Returns a vector that contain lobster path and whether its trapped

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This function updates the coordinate of each lobster at each timestep,

Description

This function updates the coordinate of each lobster at each timestep,

Usage

updateGrid(
  Lobster,
  Trap,
  trapCatch,
  lobSize,
  lobSex,
  radiusOfInfluence,
  currentZoI,
  dStep,
  howClose,
  q0,
  qmin,
  saturationThreshold,
  trapSaturation,
  lengthBased,
  lobLengthThreshold,
  sexBased
)

Arguments

Lobster	is the x & y coordinates of each lobster
Trap	is the x & y coordinates of the trap
trapCatch	number of trapped lobster
lobSize	Size of trapped lobster
lobSex	Sex of trapped lobster
radiusOfInfluence	is the initial radius of influence
currentZoI	is the bait's area of influence at each timestep
dStep	is how much a lobster moves in each time step
howClose	The area within which a lobster considered trapped
q0	is the initial probability of entry into an empty trap
qmin	is the asymptotic minimum probability of entry
saturationThreshold	is the number of lobsters in a trap at which the probability of another lobster entering the trap is zero
trapSaturation	Logical. If TRUE, lobsters behavioral interaction is included during the simulation.
lengthBased	Logical. If TRUE, lobster size is taken into account
lobLengthThreshold	is a size threshold (Carapace Length in mm), if a lobster larger than this threshold caught there will be no more entry to the trap
sexBased	Logical. If TRUE, lobster sex is taken into account and user must provide a list containing sex distribution for the simulated population

Value

a list of new coordinates, number of catch and their sizes

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