# How to use optim in R

March 12, 2013
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(This article was first published on mages' blog, and kindly contributed to R-bloggers)

A friend of mine asked me the other day how she could use the function `optim` in R to fit data. Of course there are functions for fitting data in R and I wrote about this earlier. However, she wanted to understand how to do this from scratch using `optim`.

The function `optim` provides algorithms for general purpose optimisations and the documentation is perfectly reasonable, but I remember that it took me a little while to get my head around how to pass data and parameters to `optim`. Thus, here are two simple examples.

I start with a linear regression by minimising the residual sum of square and discuss how to carry out a maximum likelihood estimation in the second example.

### Minimise residual sum of squares

I start with an x-y data set, which I believe has a linear relationship and therefore I'd like to fit y against x by minimising the residual sum of squares.

``dat=data.frame(x=c(1,2,3,4,5,6),                y=c(1,3,5,6,8,12))``

Next, I create a function that calculates the residual sum of square of my data against a linear model with two parameter. Think of `y = par[1] + par[2] * x`.

``min.RSS <- function(data, par) {              with(data, sum((par[1] + par[2] * x - y)^2))             }``

Optim minimises a function by varying its parameters. The first argument of `optim` are the parameters I'd like to vary, `par` in this case; the second argument is the function to be minimised, `min.RSS`. The tricky bit is to understand how to apply `optim` to your data. The solution is the `...` argument in `optim`, which allows me to pass other arguments through to `min.RSS`, here my data. Therefore I can use the following statement:

``result <- optim(par = c(0, 1), min.RSS, data = dat)# I find the optimised parameters in result\$par# the minimised RSS is stored in result\$valueresult## \$par## [1] -1.267  2.029## ## \$value## [1] 2.819## ## \$counts## function gradient ##       89       NA ## ## \$convergence## [1] 0## ## \$message## NULL``

Let me plot the result:

``plot(y ~ x, data = dat)abline(a = result\$par[1], b = result\$par[2], col = "red")``

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