MicrobialGrowth: MicrobialGrowth regression function
In MicrobialGrowth: Estimates Growth Parameters from Models and Plots the Curve

MicrobialGrowth

R Documentation

MicrobialGrowth regression function

Description

Regression function to different microbial growth models.

Usage

MicrobialGrowth(
  x,
  y,
  model = "gompertz",
  clip = c(-Inf, Inf),
  start = list(),
  lower = list(),
  upper = list(),
  nls.args = list(),
  callbackError = NULL,
  ...
)

Arguments

`x`	index series or time series.
`y`	values or list of values to regress (should not be logged).
`model`	wanted growth model : "baranyi", "gompertz" or "rosso".
`clip`	a pair of values indicating in which interval to clip the data `y`. When `clip` is missing, default values are used.
`start`	a named list of starting estimates. When `start` is missing, default values are used.
`lower`	a named list of lower bounds. When `lower` is missing, default values are used.
`upper`	a named list of upper bounds. When `upper` is missing, default values are used.
`nls.args`	additional parameters to use when calling nls.
`callbackError`	function to call on error during regression.
`...`	further arguments passed to or from other methods.

Details

Use listAvailableModels() function to see all values accepted by model parameter.

The default values for clip, start, lower and upper are calculated based on the given data. These default values can be known through the call member of the returned value.

The nls.args argument is a list that can contain any nls function argument except formula, algorithm, start, lower and upper which are already fixed (via a homonymous or hard-coded argument).

For the callbackError argument, prefer the stop function to block or warning to not be blocking.

Value

a MicrobialGrowth-object composed of

`call`	the matched call with several components.
`coefficients`	coefficients obtained by regression.
`data`	data used for regression, once the y values are clipped
`f`	a list of functions such as `formula` to retrieve the function of the model with the coefficients obtained by regression, `confint` to retrieve the confidence intervals, etc.
`isValid`	a boolean indicating whether the regression was successful or not.
`message`	contains the error message if the regression fails, `NULL` otherwise.
`reg`	the `nls` object returned by the `nls` function.

Examples

# Using the embedded data example_data
# Simple example
g <- MicrobialGrowth(example_data$time, example_data$y1, model="gompertz")

# Multiple regression example
G <- MicrobialGrowth(example_data$time, example_data[2:ncol(example_data)], model="gompertz")

# Example of multiple parameter changes
g <- MicrobialGrowth(example_data$time, example_data$y1, model="gompertz",
                           clip = c(0.15, Inf), start = list(N0=0.1, Nmax=2,
                           mu=0.05, lambda=40), lower = list(lambda = 40))

# Example of using `nls.args` to apply weight to some data
g <- MicrobialGrowth(example_data$time, example_data$y1, model="gompertz",
nls.args = list(weights = (function(x){(x >= 50 & x <= 70)*9 + 1})(example_data$time)))

# Example of callbackError (remaining non-blocking)
g <- MicrobialGrowth(example_data$time, example_data$y15, model="gompertz",
                           callbackError = warning)

# Example of callbackError (becoming blocking)
try(
  g <- MicrobialGrowth(c(1,2,3,4,5),c(1,1,1,1,1), model="gompertz", callbackError = stop)
)

MicrobialGrowth documentation built on April 12, 2025, 1:34 a.m.