R: Self-Starting 'nls' Michaelis-Menten Model

SSmicmen {stats}

R Documentation

Self-Starting `nls` Michaelis-Menten Model

Description

This selfStart model evaluates the Michaelis-Menten model and its gradient. It has an initial attribute that will evaluate initial estimates of the parameters Vm and K

Usage

SSmicmen(input, Vm, K)

Arguments

`input`	a numeric vector of values at which to evaluate the model.
`Vm`	a numeric parameter representing the maximum value of the response.
`K`	a numeric parameter representing the `input` value at which half the maximum response is attained. In the field of enzyme kinetics this is called the Michaelis parameter.

Value

a numeric vector of the same length as input. It is the value of the expression Vm*input/(K+input). If both the arguments Vm and K are names of objects, the gradient matrix with respect to these names is attached as an attribute named gradient.

Author(s)

José Pinheiro and Douglas Bates

Examples

PurTrt <- Puromycin[ Puromycin$state == "treated", ]
SSmicmen(PurTrt$conc, 200, 0.05)  # response only
local({  Vm <- 200; K <- 0.05
  SSmicmen(PurTrt$conc, Vm, K)    # response _and_ gradient
})
print(getInitial(rate ~ SSmicmen(conc, Vm, K), data = PurTrt), digits = 3)
## Initial values are in fact the converged values
fm1 <- nls(rate ~ SSmicmen(conc, Vm, K), data = PurTrt)
summary(fm1)
## Alternative call using the subset argument
fm2 <- nls(rate ~ SSmicmen(conc, Vm, K), data = Puromycin,
           subset = state == "treated")
summary(fm2) # The same indeed:
stopifnot(all.equal(coef(summary(fm1)), coef(summary(fm2))))

## Visualize the SSmicmen()  Michaelis-Menton model parametrization :

  xx <- seq(0, 5, length.out = 101)
  yy <- 5 * xx/(1+xx)
  stopifnot(all.equal(yy, SSmicmen(xx, Vm = 5, K = 1)))
  require(graphics)
  op <- par(mar = c(0, 0, 3.5, 0))
  plot(xx, yy, type = "l", lwd = 2, ylim = c(-1/4,6), xlim = c(-1, 5),
       ann = FALSE, axes = FALSE, main = "Parameters in the SSmicmen model")
  mtext(quote(list(phi[1] == "Vm", phi[2] == "K")))
  usr <- par("usr")
  arrows(usr[1], 0, usr[2], 0, length = 0.1, angle = 25)
  arrows(0, usr[3], 0, usr[4], length = 0.1, angle = 25)
  text(usr[2] - 0.2, 0.1, "x", adj = c(1, 0))
  text(     -0.1, usr[4], "y", adj = c(1, 1))
  abline(h = 5, lty = 3)
  arrows(-0.8, c(2.1, 2.9),
         -0.8, c(0,   5  ),  length = 0.1, angle = 25)
  text(  -0.8,     2.5, quote(phi[1]))
  segments(1, 0, 1, 2.7, lty = 2, lwd = 0.75)
  text(1, 2.7, quote(phi[2]))
  par(op)

[Package stats version 4.4.0 Index]

Self-Starting nls Michaelis-Menten Model