percentile

Calculates specified percentiles from length-frequency data.

Catch advice for data-limited vertebrate and invertebrate
fisheries managed by harvest slot limits using the SlotLim harvest
control rule. The package accompanies the manuscript "SlotLim: catch advice
for data-limited vertebrate and invertebrate fisheries managed by harvest
slot limits" (Pritchard et al., in prep). Minimum data requirements: at
least two consecutive years of catch data, length–frequency distributions,
and biomass or abundance indices (all from fishery-dependent sources);
species-specific growth rate parameters (either von Bertalanffy, Gompertz,
or Schnute); and either the natural mortality rate ('M') or the maximum
observed age ('tmax'), from which M is estimated. The following functions
have optional plotting capabilities that require 'ggplot2' installed:
prop_target(), TBA(), SAM(), catch_advice(), catch_adjust(), and
slotlim_once().

C.J. Pritchard

SlotLim

Catch Advice for Fisheries Managed by Harvest Slot Limits

percentile function

<dl><dt>LF</dt>
<dd>Numeric vector of length-frequency data (e.g., <code>data$length</code>).</dd>
<dt>probs</dt>
<dd>Numeric vector of probabilities in $[0,1]$ indicating which
percentiles to calculate. Default is <code>c(0.025, 0.975)</code> as per SlotLim.</dd>
<dt>na.rm</dt>
<dd>Logical; if <code>TRUE</code> (default), <code>NA</code>s are removed before computing
percentiles. If <code>FALSE</code>, <code>NA</code> values may propagate to the result.</dd>
<dt>sort_probs</dt>
<dd>Logical; if <code>TRUE</code> (default), <code>probs</code> are sorted ascending
(labels follow the returned order). If <code>FALSE</code>, percentiles are returned in
the input order.</dd>
<dt>unique_probs</dt>
<dd>Logical; if <code>TRUE</code> (default), duplicate <code>probs</code> are
deduplicated (first occurrence kept for labeling).</dd></dl>

Arguments

percentile — percentile

<dl>

<dt>LF</dt>
<dd>Numeric vector of length-frequency data (e.g., <code>data$length</code>).</dd>


<dt>probs</dt>
<dd>Numeric vector of probabilities in $[0,1]$ indicating which
percentiles to calculate. Default is <code>c(0.025, 0.975)</code> as per SlotLim.</dd>


<dt>na.rm</dt>
<dd>Logical; if <code>TRUE</code> (default), <code>NA</code>s are removed before computing
percentiles. If <code>FALSE</code>, <code>NA</code> values may propagate to the result.</dd>


<dt>sort_probs</dt>
<dd>Logical; if <code>TRUE</code> (default), <code>probs</code> are sorted ascending
(labels follow the returned order). If <code>FALSE</code>, percentiles are returned in
the input order.</dd>


<dt>unique_probs</dt>
<dd>Logical; if <code>TRUE</code> (default), duplicate <code>probs</code> are
deduplicated (first occurrence kept for labeling).</dd>

</dl>

percentile: percentile

Description

Usage

Value

Arguments

Details

Examples