Critical values for fishing or taxon parameters.
critical.Rdcritical_sar and critical_gpd estimates for one or more taxa the fishing intensity (sar) or gear penetration depth (gpd), above which the density/caryying capacity ratio decreases below a critical value (crit_DK).
critical_r and critical_d estimate for a combination of fishing intensity (sar) and gear penetration depth (gpd), the critical intrinsic rate of natural increase (r) or depletion fraction (d) at which the density, carrying capacity ratio reaches the critical value (crit_DK).
Usage
critical_sar (gpd = 1, fDepth = 1, uDepth = 0, d = NULL,
r = 0.1, crit_DK = 0, ...)
critical_gpd ( sar = 1, fDepth = 1, uDepth = 0, d = NULL,
r = 0.1, crit_DK = 0, ...)
critical_r (sar = 1, gpd = 1, fDepth = 1, uDepth = 0, d = NULL,
crit_DK = 0, ...)
critical_d (sar = 1, r = 0.1, crit_DK = 0, ...)Arguments
- sar
fishing intensity, estimated as Swept Area Ratio, units e.g. [m2/m2/year]. One number or a vector.
- gpd
gear penetration depth, units e.g. [cm]. One number or a vector.
- r
the intrinsic rate of natural increase of a taxon, units e.g. [/year]. One number or a vector.
- d
depletion fraction due to fishing, one value or a vector.
- crit_DK
the steady-state density over carrying capacity ratio of the taxon that need to be matched. The default value of 0 indicates that the taxon is extinct. A value of 0.01 indicates that the actual density is 1/100 of its potential density (carrying capacity).
- fDepth
fractional occurrence of species in sediment layers, dimensionless. A vector of the same length as
uDepth. The sum offDepthshould equal 1. Will be used to estimate the depletion fractiond. Will be ignored ifdis given a value.- uDepth
depth of the upper position of the sediment layers, units e.g. [cm]. A vector with length equal to the number of columns of
fDepth. Will be ignored ifdis given a value.- ...
arguments passed to the
par_dfunction
Value
These functions will either return one number, a vector or a matrix, depending on the input arguments
See also
run_perturb for how to run a disturbance model.
Traits_nioz, for trait databases in package Btrait.
MWTL for data sets on which fishing can be imposed.
map_key for simple plotting functions.
Examples
## -----------------------------------------------------------------------
## Critical sar for beam trawling for all species from the MWTL dataset
## -----------------------------------------------------------------------
gpd_mud <- 3.2 # beam trawl in muddy sediment
gpd_sand <- 1.9 # sandy
head(MWTL$fishing)
#> taxon p0 p0_5cm p5_15cm p15_30cm p30cm Age.at.maturity r
#> 1 Abludomelita obtusata 0.5 0.5 0.0 0 0 0.500000 5.120
#> 2 Abra alba 0.0 0.5 0.5 0 0 0.500000 5.120
#> 3 Abra nitida 0.0 1.0 0.0 0 0 0.500000 5.120
#> 4 Abra prismatica 0.0 1.0 0.0 0 0 2.000000 1.280
#> 5 Abra tenuis 0.0 1.0 0.0 0 0 2.000000 1.280
#> 6 Abyssoninoe hibernica 0.0 0.5 0.5 0 0 3.333333 0.768
fDepth <- MWTL$fishing[,c("p0", "p0_5cm", "p5_15cm", "p15_30cm", "p30cm")]
uDepth <- c( 0, 0, 5, 15, 30)
csar_sand <- critical_sar(gpd = gpd_sand,
fDepth = fDepth, uDepth = uDepth,
r = MWTL$fishing$r)
csar_mud <- critical_sar(gpd = gpd_mud,
fDepth = fDepth, uDepth = uDepth,
r = MWTL$fishing$r)
csar <- data.frame(taxon = MWTL$fishing$taxon,
csar_sand = csar_sand,
csar_mud = csar_mud)
summary(csar)
#> taxon csar_sand csar_mud
#> Length:400 Min. : 5.798 Min. : 3.306
#> Class :character 1st Qu.: 13.515 1st Qu.: 7.827
#> Mode :character Median : 23.852 Median : 13.896
#> Mean : 37.407 Mean : 21.606
#> 3rd Qu.: 46.388 3rd Qu.: 26.448
#> Max. :438.392 Max. :259.250
#> NA's :26 NA's :26
## -----------------------------------------------------------------------
## Critical gear penetration depth for species from the MWTL dataset
## -----------------------------------------------------------------------
fDepth <- MWTL$fishing[,c("p0", "p0_5cm", "p5_15cm", "p15_30cm", "p30cm")]
uDepth <- c( 0, 0, 5, 15, 30)
cgpd_01 <- critical_gpd(sar = 1,
fDepth = fDepth, uDepth = uDepth,
r = MWTL$fishing$r)
cgpd_10 <- critical_gpd(sar = 10,
fDepth = fDepth, uDepth = uDepth,
r = MWTL$fishing$r)
cgpd_100 <- critical_gpd(sar = 100,
fDepth = fDepth, uDepth = uDepth,
r = MWTL$fishing$r)
# sar of 100 and critical density = 10 percent
cgpd_100b <- critical_gpd(sar = 100,
fDepth = fDepth, uDepth = uDepth,
r = MWTL$fishing$r,
crit_DK = 0.1)
cgpd <- data.frame(taxon = MWTL$fishing$taxon,
cgpd_01 = cgpd_01,
cgpd_10 = cgpd_10,
cgpd_100 = cgpd_100,
cgpd_100b = cgpd_100b)
# a cgpd of 100 means: no limits
summary(cgpd)
#> taxon cgpd_01 cgpd_10 cgpd_100
#> Length:400 Min. :100 Min. : 1.127 Min. : 0.1160
#> Class :character 1st Qu.:100 1st Qu.: 2.549 1st Qu.: 0.2698
#> Mode :character Median :100 Median : 4.778 Median : 0.5319
#> Mean :100 Mean : 5.465 Mean : 1.0229
#> 3rd Qu.:100 3rd Qu.: 7.286 3rd Qu.: 0.9075
#> Max. :100 Max. :20.095 Max. :15.3686
#> NA's :8 NA's :8 NA's :8
#> cgpd_100b
#> Min. : 0.1044
#> 1st Qu.: 0.2430
#> Median : 0.4792
#> Mean : 0.9566
#> 3rd Qu.: 0.8188
#> Max. :15.3321
#> NA's :8