segmented_plate: Call 'segmented' for selected wells.

In raim/platexpress: Inspection and Analysis of Microbial Growth and Gene Expression Data

Description

The package segmented splits curves into linear segments, given a list of pre-defined breakpoints. If the passed data is a biomass measure (eg. OD), and option log=TRUE the slopes correspond to local growth rate (per time unit). Missing (NA) or non-finite y-values will be removed. segmented has a random initialization and sometimes fails. The function will attempt maxtry of calls before giving up.

Usage

segmented_plate(
  data,
  yid = "OD",
  wells,
  log = TRUE,
  xid,
  man = 1,
  maxtry = 5,
  control = segmented::seg.control(),
  psis,
  psi,
  npsi = 5,
  plot = FALSE,
  verb = 0,
  ...
)

Arguments

data	platexpress data object
yid	ID of the platexpress data to use
wells	subset and plot order of wells
log	use ln of the data
xid	x-axis data ID in platexpress data
man	apply a moving average ma with n=man
maxtry	maximum number of attempts to run segmented
control	a list of parameters for controlling the segmented fitting process. See the documentation for seg.control for details.
psis	named list of breakpoints for wells, generated from argument psi if missing
psi	vector of breakpoints (x-values) to be passed to segmented, generated as equal spaced breakpoints from argument npsi if missing
npsi	number of equally spaced breakpoints, used if both psis and psi are missing
plot	plot each fit
verb	progress messages
...	arguments passed to segmented

raim/platexpress documentation built on Jan. 18, 2022, 1:41 p.m.