SSmicmen

0th

Percentile

Self-Starting Nls Michaelis-Menten Model

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

Keywords
models
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.

See Also

nls, selfStart

Aliases
  • SSmicmen
Examples
library(stats) # NOT RUN { 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, len = 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) # }
Documentation reproduced from package stats, version 3.5.0, License: Part of R 3.5.0

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