Fit a primary growth model — fit

fit_growth() validates the input data, builds the nonlinear model formula, fits it with gslnls::gsl_nls(), and returns a predmicror_fit object.

Usage

fit_growth(data, model, time, response = "lnN", start, ...)

Arguments

data: A data frame containing the time and response variables.
model: A model name, either quoted or unquoted. See predmicror_models().
time: Column containing time values, either quoted or unquoted.
response: Column containing the response values, either quoted or unquoted. Defaults to "lnN".
start: Named list of initial parameter values for the selected model.
...: Additional arguments passed to gslnls::gsl_nls().

Value

A predmicror_fit object with the fitted model and metadata.

Details

Growth models expect the response to be the natural logarithm of the microbial concentration, usually lnN.

Examples

data(growthfull)
fit <- fit_growth(
  growthfull,
  model = "HuangFM",
  time = "Time",
  response = "lnN",
  start = list(Y0 = 0, Ymax = 22, MUmax = 1.7, lag = 5)
)
coef(fit)
#>          Y0        Ymax       MUmax         lag 
#>  0.04562398 21.13231520  1.85942431  5.07986566