r - How to plot raw data and add predict + confidence intervals using maximum likelihood function in R gpplot2?

Question

I'm trying to plot the raw data along with the curve and confidence intervals for maximum likelihood model function in R. My data is stored in df(x.number, y.size). I'm trying to run MLL using skewfunc.

I want to use estimates from the model to plot the curve + 95% confidence intervals along with the raw data, but I am not sure how to proceed:

1. It's not a regular polynomial so I can't use the geom_smooth function.
2. The function also has a ifelse that complicates matters.
3. I'm also unclear on how to extract the 95% confidence intervals from the model.

library(stats4)
library(ggplot2)

y.size <- c(2.69,4.1,8.04,3.1,5.27,5.033333333,3.2,7.25,6.29,4.55,6.1,2.65,3.145,3.775,3.46,5.73,5.31,4.425,3.725,4.32,5,3.09,5.25,5.65,3.48,6.1,10,9.666666667,6.06,5.9,2.665,4.32,3.816666667,3.69,5.8,5,3.72,3.045,4.485,3.642857143,5.5,6.333333333,4.75,6,7.466666667,5.03,5.23,4.85,5.59,5.96,5.33,4.92,4.255555556,6.346666667,4.13,6.33,4,7.35,6.35,4.63,5.13,7.4,4.28,4.233333333,4.3125,6.18,4.3,4.47,4.88,4.5,2.96,2.1,3.7,3.62,5.42,3.8,5.5,3.27,3.36,3.266666667,2.265,3.1,2.51,2.51,4.4,2.64,4.38,4.53,2.29,2.87,3.395,3.26,2.77,3.22,4.31,4.73,4.05,3.48,4.8,4.7,3.05,4.21,5.95,4.39,4.55,4.27,4.955,4.65,3.32,3.48,3.828571429,4.69,4.68,3.76,3.91,4,4.41,4.19,4.733333333,4.32,2.83,3.41,4.42,3.47,3.84,4.39)
    
x.number <- c(69,62,8,80,13,12,2,22,19,49,840,44,31,56,33,58,91,8,15,86,11,69,12,24,32,27,1,4,26,4,28,33,1516,41,20,58,44,29,58,14,3,3,6,3,26,52,26,29,92,30,18,11,27,19,38,78,57,52,17,45,56,7,37,7,14,13,164,76,82,14,273,122,662,434,126,374,1017,522,374,602,164,5,191,243,134,70,23,130,306,516,414,236,172,164,92,53,50,17,22,27,92,48,30,55,28,296,35,12,350,17,22,53,97,62,92,272,242,170,37,220,452,270,392,314,150,232)
df <- data.frame(x.number, y.size)
df <- df[df$x.number < 750,] #data

aa = -1.02 ; K = 12; Ka = 15; q = -0.9; sigma = 0.1
skewfun <- function(aa, K, Ka, q, sigma){
  p <- df$x.number / K
  lnqp <- if (q == 0) log(p) else (p^q - 1) / q
  y.pred <- (aa * (p * K / Ka - 1) - 1) * lnqp
  ll <-   -sum(dnorm(y.size, mean = y.pred, sd = sigma, log=TRUE ))
  ll
}

mle2.model <- mle(skewfun, start = list(aa = -1.02, K = 12, Ka = 15, q = -0.9, sigma = 0.1))
summary(mle2.model)
-logLik(mle2.model)
AIC(mle2.model)

ggplot(data=df,aes(x=x.number,y=y.size))+ 
  geom_point() #Raw Data

标签： rggplot2