d_gcfit: Wrapper function for automated growth curve fitting

In dcangst/fitr: Bacterial Growth Rate Estimation in R

Wrapper function for automated growth curve fitting

Description

Wrapper function for automated growth curve fitting

Function for blanking OD data & flagging growth/no growth

Arguments

w_size	size of sliding window (number of datapoints considered)
time_name	name of column containing times (in units after start of experiment)
trafo	Data transformation, one of "logNN0" (for log(N/N0)), "log" or "none".
logBase	Base for logarithmitic transformation if trafo != "none", defaults to 2.
min_numP	minimum number of points for fit to be acceptable, defaults to "w_size"
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). Requires data of class "fitr_data"
RsqCutoff	Only fits with a correlation coefficient higher than the cutoff are considered. Defaults to 0.95.
parallel	if TRUE, apply function in parallel, using parallel backend provided by foreach.
progress	name of the progress bar to use, see create_progress_bar
...	additional parameters passed to ply functions.
data	long-form data frame with growth data, must contain column named ID with a unique ID for each curve.
group	name of grouping variable (e.g. plates for which blanks must be seperate), a factor.
od_name	name of column containing OD values
bl_col	name of column containing well description, e.g. "strain"
bl_name	which wells are blanks?, e.g. "bl"
cutoff	discard values <= cutoff

Output

an object of class fitr.

long-form data frame with additional columns od_name_bl (blanked OD values) and QCgrowth (logical)

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