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Cardinal model for pH

Source: R/cardinal_ph.R
CMPH.Rd

CMPH function to fit the pH cardinal model (Rosso et al, 1993). Returns the model parameters estimated according to data collected in microbial growth experiments.

Usage

CMPH(x, pHmax, pHmin, MUopt, pHopt)

Arguments

x

is a numeric vector indicating the pH of the experiment

pHmax

is the maximum pH for growth

pHmin

is the minimum pH for growth

MUopt

is the optimum growth rate

pHopt

is the optimum pH for growth

Value

An object of nls class with the fitted parameters of the model

Details

The model's inputs are:

x: pH

sqrtGR: the square root of the growth rate ($time^-1$)

Users should make sure that the growth rate input is entered after a square root transformation, sqrGR = sqrt(GR).

References

Rosso L, Lobry J, Charles (Bajard) S, Flandrois J (1995). “Convenient Model To Describe the Combined Effects of Temperature and pH on Microbial Growth.” Applied and environmental microbiology, 61, 610–6. doi:10.1128/AEM.61.2.610-616.1995 .

Author

Vasco Cadavez vcadavez@ipb.pt and Ursula Gonzales-Barron ubarron@ipb.pt

Examples

library(gslnls)
data(ph)
initial_values = list(pHmax=9, pHmin=3, MUopt=1.0, pHopt=7)
fit <- gsl_nls(sqrtGR ~ CMPH(pH,pHmax,pHmin,MUopt,pHopt),
               data=ph,
               start =  initial_values)
summary(fit)
#> 
#> Formula: sqrtGR ~ CMPH(pH, pHmax, pHmin, MUopt, pHopt)
#> 
#> Parameters:
#>       Estimate Std. Error t value Pr(>|t|)    
#> pHmax  9.34191    0.04002  233.42  < 2e-16 ***
#> pHmin  4.37859    0.01484  295.10  < 2e-16 ***
#> MUopt  1.05158    0.04180   25.16 2.26e-10 ***
#> pHopt  7.31579    0.08769   83.42 1.50e-15 ***
#> ---
#> Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1
#> 
#> Residual standard error: 0.04141 on 10 degrees of freedom
#> 
#> Number of iterations to convergence: 28 
#> Achieved convergence tolerance: 2.045e-13
#>