https://github.com/cran/bbmle
Raw File
Tip revision: a9e88f404068e23c6e0b8a1b2aa818082639db1a authored by Ben Bolker on 22 August 2013, 00:00:00 UTC
version 1.0.13
Tip revision: a9e88f4
optimizers.Rout.save

R Under development (unstable) (2013-08-18 r63609) -- "Unsuffered Consequences"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: i686-pc-linux-gnu (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(bbmle)
Loading required package: stats4
> old_opts <- options(digits=3)
> x <- 0:10
> y <- c(26, 17, 13, 12, 20, 5, 9, 8, 5, 4, 8)
> d <- data.frame(x,y)
> suppressWarnings(fits <- lapply(c("optim","nlm","nlminb"),
+                mle2,
+                minuslogl=y~dpois(lambda=ymax/(1+x/xhalf)),
+                start=list(ymax=15,xhalf=6),data=d,
+                method="Nelder-Mead")) ## 'method' is ignored by nlm()/nlminb()
> 
> sapply(fits,coef)
       [,1]  [,2]  [,3]
ymax  25.00 25.00 25.00
xhalf  3.06  3.06  3.06
> sapply(fits,logLik)
[1] -28.6 -28.6 -28.6
> 
> (fit2 <-  mle2(y~dpois(lambda=25/(1+x/xhalf)),
+               start=list(xhalf=5),data=d,
+               lower=2,upper=8,
+               optimizer="optimize"))

Call:
mle2(minuslogl = y ~ dpois(lambda = 25/(1 + x/xhalf)), start = list(xhalf = 5), 
    optimizer = "optimize", data = d, lower = 2, upper = 8)

Coefficients:
xhalf 
 3.06 

Log-likelihood: -28.6 
> 
> ## gives error referring to 'interval' rather than 'upper'/'lower'
> ## (fit2 <-  mle2(y~dpois(lambda=25/(1+x/xhalf)),
> ##              start=list(xhalf=5),
> ##              optimizer="optimize"))
> options(old_opts)
> 
> proc.time()
   user  system elapsed 
  0.536   0.848   2.784 
back to top