calcPercChange: calcPercChange

In Pacific-salmon-assess/WSP-Metrics-Pkg: WSPMetrics Package: R package to calculate and use metrics for status assessments under Canada's Wild Salmon Policy (WSP)

calcPercChange

Description

This function applies the calculation of percent change in abundance over time to a data frame (Year x Stock) iteratively for each year of the time-series using only the data prior to that year. It calculate declines over a specified number of generation and uses an exponential model to estimate decline rate, as per IUCN guidelines. For a single vector use calcPercChangeSimple() to calculate percent declines over the entire time period.

Usage

calcPercChange(
  X,
  gen.in = 4,
  slope.num.gen = 3,
  extra.yrs = 0,
  genmean.smoothing = TRUE,
  log.transform = TRUE,
  out.exp = TRUE,
  tracing = FALSE
)

Arguments

X	a data frame of raw values with dimensions Years x Stocks. Row labels are years. NAs values are allowed.
gen.in	= average generation time
slope.num.gen	number of generations over which to calculate the perc change
extra.yrs	to handle COSEWIC "extra year". default is 0
genmean.smoothing	if TRUE, apply the smoothSeries() function. default is TRUE
log.transform	if TRUE, log-transform the time series before calculating the smoothed series. default is TRUE
out.exp	if TRUE, take the exponent of the smoothed series for output. default is TRUE
tracing	if TRUE, print various diagnostics to the command line. default is FALSE

Pacific-salmon-assess/WSP-Metrics-Pkg documentation built on July 16, 2025, 1:46 p.m.