lag_time: Calculate lag time
In gcplyr: Wrangle and Analyze Growth Curve Data

lag_time

R Documentation

Calculate lag time

Description

Lag time is calculated by projecting a tangent line at the point of maximum (per-capita) derivative backwards to find the time when it intersects with the minimum y-value

Usage

lag_time(
  x = NULL,
  y = NULL,
  deriv = NULL,
  blank = NULL,
  trans_y = "log",
  na.rm = TRUE,
  slope = NULL,
  x1 = NULL,
  y1 = NULL,
  y0 = NULL,
  warn_logtransform_warnings = TRUE,
  warn_logtransform_infinite = TRUE,
  warn_min_y_mismatch = TRUE,
  warn_multiple_maxderiv = TRUE,
  warn_one_lag = TRUE,
  warn_no_lag = TRUE,
  warn_blank_length = TRUE
)

Arguments

`x`	Vector of x values (typically time)
`y`	Vector of y values (typically density)
`deriv`	Vector of derivative values (typically per-capita derivative)
`blank`	y-value associated with a "blank" where the density is 0. Is required when `trans_y = TRUE`. A vector of blank values may be specified only when all of `slope`, `x1`, `y1`, and `y0` are provided as vectors
`trans_y`	One of `c("linear", "log")` specifying the transformation of y-values. `'log'` is the default, producing calculations of lag time assuming a transition to exponential growth `'linear'` is available for alternate uses
`na.rm`	a logical indicating whether missing values or values that become `NA` or infinite during log-transformation should be removed
`slope`	Slope to project from x1,y1 to y0 (typically per-capita growth rate). If not provided, will be calculated as `max(deriv)`
`x1`	x value (typically time) to project slope from. If not provided, will be calculated as `x[which.max(deriv)]`.
`y1`	y value (typically density) to project slope from. If not provided, will be calculated as `y[which.max(deriv)]`.
`y0`	y value (typically density) to find intersection of slope from x1, y1 with. If not provided, will be calculated as `min(y)`
`warn_logtransform_warnings`	logical whether warning should be issued when log(y) produced warnings.
`warn_logtransform_infinite`	logical whether warning should be issued when log(y) produced infinite values that will be treated as `NA`.
`warn_min_y_mismatch`	logical whether warning should be issued when `min(y)` does not equal `min(y[!is.na(x)])`.
`warn_multiple_maxderiv`	logical whether warning should be issued when there are multiple points in `deriv` that are tied for the highest, and only the first will be used.
`warn_one_lag`	logical whether warning should be issued when some, but not all, inputs are vectorized, and only one lag time value will be returned.
`warn_no_lag`	logical whether warning should be issued when calculated lag time is less than the minimum value of x.
`warn_blank_length`	logical whether warning should be issued when an unexpected number of `blank` values was provided and only the first will be used

Details

For most typical uses, simply supply x, y, and deriv (using the per-capita derivative and trans_y = 'log').

Advanced users may wish to use alternate values for the slope of the tangent line (slope), origination point of the tangent line (x1, y1), or minimum y-value y0. If specified, these values will override the default calculations. If and only if all of slope, x1, y1, and y0 are provided, lag_time is vectorized on their inputs and will return a vector of lag time values.