cmsy: Catch-MSY method
In datalimited/datalimited: Stock Assessment Methods for Data-limited Fisheries

Description Usage Arguments Value References Examples

Apply the catch-MSY method from Martell and Froese (2013).

cmsy(yr, ct, interyr_index = 2L, interbio = c(0, 1), bio_step = 0.05,
  start_r = resilience(NA), start_k = c(max(ct), 50 * max(ct)),
  startbio = if (ct[1]/max(ct) < 0.2) c(0.5, 0.9) else c(0.2, 0.6),
  sig_r = 0.05, reps = 1e+05, revise_bounds = TRUE, finalbio = if
  (ct[length(ct)]/max(ct) > 0.5) c(0.3, 0.7) else c(0.01, 0.4))

`yr`	Numeric vector of years
`ct`	Numeric vector of catch
`interyr_index`	Index of the interim year within time series for which biomass estimate is available
`interbio`	A numeric vector that gives the lower and upper biomass limits in the interim year
`bio_step`	Step size between lower and upper biomass limits in the iterim year
`start_r`	A numeric vector of length 2 giving the lower and upper bounds on the population growth rate parameter. This can either be specified manually or by translating resiliency categories via the function `resilience`
`start_k`	Numeric vector of length 2 giving the lower and upper starting bounds on stock biomass at carrying capacity
`startbio`	Starting biomass depletion
`sig_r`	Standard deviation of process noise
`reps`	Number of repititions to run the sampling
`revise_bounds`	Should the bounds on r and k be revised after fitting the algorithm once? The algorithm will then fit a second time with the revised bounds.
`finalbio`	Maximum and minimum biomass depletion in the final year

A list containing a matrix biomass; bmsy, msy, and mean_ln_msy management quantities; and a data frame theta with the intrinsic population growth rate r, carrying capacity k, binomial likelihood ell (filtered to include only those with a value of 1, and the starting biomass depletion J. In the biomass matrix, each row contains an iteration and each column contains a year.

Martell, S., & Froese, R. (2013). A simple method for estimating MSY from catch and resilience. Fish and Fisheries, 14(4), 504-514. http://doi.org/10.1111/j.1467-2979.2012.00485.x

# An example using cmsy() with a stock from the RAM Legacy database:
# The stock is "BGRDRSE" (Blue Grenadier Southeast Australia)

x <- cmsy(blue_gren$yr, ct = blue_gren$ct, reps = 2e4)
head(x$theta)
par(mfrow = c(2, 2))
plot(blue_gren$yr, blue_gren$ct, type = "o", xlab = "Year", ylab = "Catch (t)")
plot(blue_gren$yr,  apply(x$biomass, 2, median)[-1], type = "o",
  ylab = "Estimated biomass", xlab = "Year")
hist(x$bmsy)
plot(x$theta$r, x$theta$k)
library("ggplot2")
ggplot(x$bbmsy, aes(year, bbmsy_q50)) + geom_line()  +
    geom_ribbon(aes(ymin = bbmsy_q25, ymax = bbmsy_q75), alpha = 0.2) +
    geom_ribbon(aes(ymin = bbmsy_q2.5, ymax = bbmsy_q97.5), alpha = 0.1) +
    geom_hline(yintercept = 1, lty = 2)