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Last data update: 2014.03.03

R: E_MSY_0.1: Exploitation indices

E_MSY_0.1

R Documentation

E_MSY_0.1: Exploitation indices

Description

E_MSY_0.1 computes two indices of exploitation: Emsy or Fmsy (maximum sustainable yield), and E0.1 or F0.1 ("start" of full exploitation) per TL class.

Usage

E_MSY_0.1(data, Mul_eff=NULL, B.Input=NULL, Beta=NULL,
	TopD=NULL, FormD=NULL, TLpred=NULL, maxTL=NULL)

Arguments

`data`	is the list object returned by the create.ETmain function.
`Mul_eff`	is a parameter of the create.ETdiagnosis function. It is a vector of fishing effort multipliers that the user wants to test. Mul_eff must contain the value 1 (reference state). By default, the function simulates a range of fishing effort multipliers from 0 to 5 for each fleet.
`B.Input`	is a parameter of the create.ETdiagnosis function. It is a logical argument (default=F), if TRUE the "Biomass input control" equation is accounted for in EcoTroph equations.
`Beta`	is a parameter of the create.ETdiagnosis function. It is a coefficient expressing the extent of the biomass input control. Beta=0 refers to an ecosystem where all secondary production originates from grazing on primary producers, and Beta=1 to an ecosystem where detritus and/or recruitment contribute to a major part of the biomass input (default=0.2).
`TopD`	is a parameter of the create.ETdiagnosis function. It is a coefficient expressing the top-down control, i.e. the fraction of the natural mortality depending on predator abundance. It varies between 0 and 1. The user can specify a numeric value, which is applied to each trophic level, or a numeric vector (of the same length as TL classes), i.e. a value for each TL (default=0.4).
`FormD`	is a parameter of the create.ETdiagnosis function. It is a shape parameter varying between 0 and 1. It defines the functional relationship between prey and predators. The value 1 refers to a situation where predators abundance has a linear effect on the speed of the flow of their preys. The user can specify a numeric value, which is applied to each trophic level, or a numeric vector (of the same length as TL classes), i.e. a value for each TL (default=0.5).
`TLpred`	is a parameter of the create.ETdiagnosis function. It is the trophic level that the user considers to be the "predator" trophic classes start. The default value is 3.5.
`maxTL`	is a numeric string indicating the maximum TL for which indices are computed.

Details

For any TL class, if E0.1 and/or Emsy value(s) is(are) equal to the maximum effort multiplier tested (max(Mul_eff)), then E/F0.1 and/or E/Fmsy are set equal to NA.

Value

The E_MSY_0.1 function returns a data.frame containing Fmsy, Emsy, F0.1 and E0.1 per TL class.

Author(s)

Gatti Paul, Colleter Mathieu, Guitton Jerome.

Examples

data(ecopath_guinee)
E_MSY_0.1(create.ETmain(ecopath_guinee))

Results


R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(EcoTroph)
Loading required package: XML
> png(filename="/home/ddbj/snapshot/RGM3/R_CC/result/EcoTroph/E_MSY_0.1.Rd_%03d_medium.png", width=480, height=480)
> ### Name: E_MSY_0.1
> ### Title: E_MSY_0.1: Exploitation indices
> ### Aliases: E_MSY_0.1
> ### Keywords: ~EcoTroph ~Diagnosis
> 
> ### ** Examples
> 
> data(ecopath_guinee)
> ## No test: 
> E_MSY_0.1(create.ETmain(ecopath_guinee))
        F_MSY E_MSY        F_0.1 E_0.1
1          NA    NA           NA    NA
2          NA    NA 6.183388e-15   7.8
2.1        NA    NA 8.200517e-06   7.1
2.2        NA    NA 6.575913e-04   6.5
2.3        NA    NA 2.081360e-02   5.0
2.4        NA    NA 8.832019e-01   2.3
2.5        NA    NA 1.226859e+00   2.0
2.6        NA    NA 1.245550e+00   2.6
2.7        NA    NA 9.794597e-01   8.6
2.8        NA    NA 4.184343e-01   9.9
2.9        NA    NA 2.551071e-01   9.9
3          NA    NA 2.375439e-01   9.9
3.1        NA    NA 3.233783e-01   9.9
3.2        NA    NA 4.764017e-01   9.5
3.3        NA    NA 4.044676e-01   5.4
3.4 0.8580620   8.1 3.707675e-01   3.5
3.5 0.7538524   5.3 3.698144e-01   2.6
3.6 0.7220788   4.0 3.610394e-01   2.0
3.7 0.6703626   3.1 3.459936e-01   1.6
3.8 0.6142202   2.5 3.439633e-01   1.4
3.9 0.5605067   2.1 3.202896e-01   1.2
4   0.5034486   1.8 2.796937e-01   1.0
4.1 0.4843026   1.7 2.563955e-01   0.9
4.2 0.4255743   1.5 2.553446e-01   0.9
4.3 0.4162800   1.5 2.220160e-01   0.8
4.4 0.3746789   1.4 2.141022e-01   0.8
4.5 0.3574266   1.4 2.042438e-01   0.8
4.6 0.3141393   1.3 1.933165e-01   0.8
4.7 0.2957439   1.3 1.819962e-01   0.8
4.8 0.2774625   1.3 1.494029e-01   0.7
4.9 0.2397727   1.2 1.398674e-01   0.7
5   0.2241804   1.2 1.307719e-01   0.7
5.1 0.1919878   1.1 1.221741e-01   0.7
5.2 0.1792822   1.1 1.140887e-01   0.7
5.3 0.1673694   1.1 9.129242e-02   0.6
5.4 0.1420187   1.0 8.521124e-02   0.6
5.5 0.1192910   0.9 7.952732e-02   0.6
> ## End(No test)
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>