growthrates (version 0.8.1)

all_easylinear: Easy Growth Rates Fit to data Frame

Description

Determine maximum growth rates from log-linear part of the growth curve for a series of experiments.

Usage

all_easylinear(...)
# S3 method for formula
all_easylinear(formula, data, h = 5, quota = 0.95,
  subset = NULL, ...)
# S3 method for data.frame
all_easylinear(data, grouping, time = "time",
  y = "value", h = 5, quota = 0.95, ...)

Arguments

…

generic parameters, reserved for future extensions.

formula

model formula specifying dependent, independent and grouping variables in the form: dependent ~ independent | group1 + group2 + ….

data

data frame of observational data.

h

with of the window (number of data).

quota

part of window fits considered for the overall linear fit (relative to max. growth rate).

subset

a specification of the rows to be used: defaults to all rows.

grouping

model formula or character vector of criteria defining subsets in the data frame.

time

character vectors with name independent variabl.e.

y

character vector with name of dependent variable

Value

object with parameters of all fits.

References

Hall, BG., Acar, H, Nandipati, A and Barlow, M (2014) Growth Rates Made Easy. Mol. Biol. Evol. 31: 232-38, 10.1093/molbev/mst187

See Also

Other fitting functions: all_growthmodels, all_splines, fit_easylinear, fit_growthmodel, fit_spline

Examples

# NOT RUN {
# }
# NOT RUN {
library("growthrates")
L <- all_easylinear(value ~ time | strain + conc + replicate, data=bactgrowth)
summary(L)
coef(L)
rsquared(L)

results <- results(L)

library(lattice)
xyplot(mumax ~ conc|strain, data=results)
# }
# NOT RUN {
# }