self start for profile decay function
Self starter for a decay of a variable within a canopy (e.g. nitrogen concentration).
profd(x, a, b, c, d) SSprofd(x, a, b, c, d)
x |
input vector (x) |
a |
represents the maximum value |
b |
represents the minimum value |
c |
represents the rate of decay |
d |
represents an empirical coefficient which provides flexibility |
This function is described in Archontoulis and Miguez (2015) - (doi:10.2134/agronj2012.0506) and originally in Johnson et al. (2010) Annals of Botany 106: 735–749, 2010. (doi:10.1093/aob/mcq183).
a numeric vector of the same length as x containing parameter estimates for equation specified
profd: vector of the same length as x using the profd function
require(ggplot2) set.seed(1234) x <- 1:10 y <- profd(x, 0.3, 0.05, 0.5, 4) + rnorm(10, 0, 0.01) dat <- data.frame(x = x, y = y) fit <- nls(y ~ SSprofd(x, a, b, c, d), data = dat) ## plot ggplot(data = dat, aes(x = x, y = y)) + geom_point() + geom_line(aes(y = fitted(fit))) ## profiling ## It does not work at a lower alphamax level ## Use this if you want to look at all four parameters ## par(mfrow=c(2,2)) plot(profile(fit, alphamax = 0.016)) ## Reset graphical parameter as appropriate: par(mfrow=c(1,1)) ## parameter 'd' is not well constrained confint(fit, level = 0.9)
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