R/plot_uclnegobs.r
plot_uclnegobs.Rdplot_uclnegobs plots upper confidence limit of total bycatch vs
observer coverage when no bycatch is observed, given total fishery effort,
dispersion index, and confidence level. The function returns (1) minimum
observer coverage needed to fall within user-specified upper confidence
limit for bycatch when none was observed, and/or (2) the upper confidence
limit for bycatch given specified observer coverage and no observed bycatch.
plot_uclnegobs(te, d = 2, cl = 95, targetucl = 0, fixedoc = 0,
ymax = 100, showplot = TRUE, silent = FALSE, ...)an integer greater than 1. Total effort in fishery (e.g., trips or sets).
a number greater than or equal to 1. Dispersion index. The dispersion
index corresponds to the variance-to-mean ratio of effort-unit-level bycatch,
so d = 1 corresponds to Poisson-distributed bycatch, and d > 1
to overdispersed bycatch.
a non-negative number less than or equal to 100. Confidence level for upper confidence limit of total bycatch (as percentage), given no bycatch observed.
a non-negative number. Target maximum upper confidence limit for total bycatch given zero bycatch observed. If set to 0, no corresponding minimum observer coverage will be highlighted or returned.
a non-negative number between 0 and 100. Percent observer coverage for which to return ucl value.
a positive number. Upper limit for y-axis of plot.
logical. If FALSE, plotting is suppressed.
logical. If TRUE, print output to terminal is suppressed.
additional arguments for compatibility with Shiny.
A list with components:
a data frame with the following fields for each coverage level included:
number of observed effort units (nobs),
proportion observer coverage (pobs),
upper confidence limit of total bycatch given none observed (ucl),
and finite population correction (fpc) used in calculating ucl.
specified target maximum upper confidence limit of bycatch.
minimum observer coverage (as percentage) for which upper
confidence limit of bycatch is targetucl when none observed.
specified percentage observer coverage for which upper confidence limit of bycatch is returned.
observer coverage (as effort) corresponding to fixedoc.
upper confidence limit of total bycatch corresponding
to zero bycatch observed in fixedoc coverage.
specified total effort.
specified dispersion index.
specified confidence level.
Returned invisibly.
Upper confidence limits are based on the probability density function for
the corresponding Poisson or negative binomial distribution. Upper confidence
limits based on d+/-1 (as allowed by specification of d) are also plotted.
If fixedoc specified, corresponding upper confidence limit is provided
in printed output and returned object, but not in plot.
Caveat: plot_uclnegobs assumes that (1) observer coverage is
representative, (2) bycatch is in terms of individuals (not weight) per unit
effort,and (3) the specified dispersion index reflects the highest level of
any hierarchical variance (e.g., using dispersion index at trip level if
greater than that at set level). Violating these assumptions will likely
result in negatively biased projections of the observer coverage needed to
meet a specified objective. More conservative (higher) projections can be
obtained by using a higher dispersion index d. Users may want to
explore uncertainty in dispersion index and in bycatch per unit effort by
varying those inputs.