calcMetrics: calcMetrics

In SOLV-Code/MetricsCOSEWIC: Metrics for COSEWIC status assessments.

calcMetrics

Description

Main function that applies all the individual metric functions and produces a summary output

Usage

calcMetrics(
  series.in,
  yrs.in,
  gen.in,
  stk.label = "Stock",
  species.label = "Species",
  series.label = "DataVersion",
  slope.specs = list(num.gen = 3, extra.yrs = 0, filter.sides = 1, log.transform =
    TRUE, out.exp = TRUE, na.rm = FALSE),
  avg.specs = list(avg.type = "geomean", recent.excl = FALSE, min.lt.yrs = 20),
  metric.bm = list(RelAbd = c(NA, NA), AbsAbd = c(1000, 10000), LongTrend = c(0.5,
    0.75), PercChange = c(-25, -15), ProbDeclBelowLBM = c(NA, NA)),
  retro.start = NULL,
  tracing = TRUE
)

Arguments

series.in	vector with numeric values
yrs.in	vector of years corresponding to the values in series.in (missing yrs need to be included as NA values in series.in)
gen.in	integer value with avg generation time
stk.label	label to be used in output file (e.g. "EStu")
species.label	label to be used in output file (e.g. "Sk")
series.label	label to be used in output file (e.g. "LogSm_TotSpn")
slope.specs	list with arguments for the slope function NAME, see details there
avg.specs	list with arguments for the avg function NAME, see details there
metric.bm	list with upper and lower benchmarks for each metric
retro.start	user-specified year. if NULL, do retrospective for last 9 yrs of the series
tracing	if TRUE, print lots of diagnostic/tracking info to the command lines

SOLV-Code/MetricsCOSEWIC documentation built on Nov. 3, 2022, 8:59 p.m.