gcfit: Estimate growth rate from growth curve

In dcangst/fitr: Bacterial Growth Rate Estimation in R

Estimate growth rate from growth curve

Description

fits a a linear model over a sliding window to growth data. Outputs all fits as a data.frame

Usage

gcfit(
  data,
  w_size,
  od_name,
  time_name,
  trafo = "log",
  logBase = 2,
  growthCheck = "none",
  blankSD = NA
)

Arguments

data	long-form data frame with growth data.
w_size	size of sliding window (number of datapoints).
od_name	name of column containing OD values.
time_name	name of column containing times (in units after start of experiment).
trafo	Data transformation, one of "logNN0" (for log(N/N0) transformation), "log" or "none".
logBase	Base for logarithmitic transformation if trafo != "none", defaults to 2.
growthCheck	Check whether there was growth at all. One of "none" (no Check), "sd2" (Growth only if difference between minimal and maximal OD is larger than twice the standard deviation of the blanks).
blankSD	standard deviation of blanks appropriate to this curve, required if "growthCheck" = "sd2"

Output

data.frame of with all fits for all possible windows

dcangst/fitr documentation built on Sept. 9, 2022, 3:30 p.m.