MicrobialGrowth (version 1.0.0)

MicrobialGrowth.create: MicrobialGrowth create function

Description

MicrobialGrowth-object creator from the 4 biological meaning parameters.

Usage

MicrobialGrowth.create(
  N0,
  Nmax,
  mu,
  lambda,
  xlim,
  model = "gompertz",
  n = 101,
  ...
)

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

always with this method.

reg

always with this method.

Arguments

N0

initial population.

Nmax

final/maximum population.

mu

growth rate.

lambda

latency time.

xlim

range of values to simulate x and y (and hence plotting, etc.)

model

wanted growth model: "baranyi", "gompertz" or "rosso"

n

number of points to simulate in the interval xlim.

...

further arguments passed to or from other methods.

Details

The N0, Nmax, mu and lambda parameter-coefficients can be given as one to three values.

A single value means that the coefficient and the confidence interval values will be identical.

Two values means that they will correspond to the confidence interval, and the coefficient will be calculated as the average of these two values.

Three values means that each of these values will be associated with the coefficient or the confidence interval.

Values are always sorted automatically, which means that c(2,1,3) is equivalent to c(1,2,3).

Examples

# Simple example
g <- MicrobialGrowth.create(N0 = 0.14, Nmax = 1.43, mu = 0.07, lambda = 45,
     xlim = c(0, 100), model="gompertz")

# Example from a regression (whose values can be stored and then reused later)
g <- MicrobialGrowth(example_data$time, example_data$y1, model="gompertz")
c <- g$coefficients
g2 <- MicrobialGrowth.create(c$N0, c$Nmax, c$mu, c$lambda,
      xlim = c(min(g$data$x),max(g$data$x)), n = length(g$data$x), model="gompertz")

# Example with confidence intervals
g <- MicrobialGrowth.create(N0 = c(0.13, 0.15), Nmax = 1.43, mu = c(0.05, 0.07, 0.09),
lambda = c(45, 49, 43), xlim = c(0, 100), model="gompertz")
# Coefficient N0 is 0.14 and the confidence interval is (0.13, 0.15)
# Coefficient Nmax is 1.43 and the confidence interval is (1.43, 1.43)
# Coefficient mu is 0.07 and the confidence interval is (0.05, 0.09)
# Coefficient lambda is 45 and the confidence interval is (43, 49)