View source: R/Module_calcMetrics.R
calcMetrics | R Documentation |
Main function that applies all the individual metric functions and produces a summary output
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 )
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 |
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