Maximum likelihood part 1

This is the first in a series of posts about maximum likelihood methods for fitting statistical models to data. Inspiration for the material comes in large part from Drew Purves who presented something similar. Owen is using Drew’s approach as the basis for this course. Much of the R specific stuff is heavily influenced by Ben Bolker’s excellent book: Ecological Models and Data in R. The goal of this and the following posts includes: learning how to fit to our data more mechanistic models of arbitrary complexity.

Why adjust your r-squared

Just a little demo of what happens if you don’t or do adjust your r-squared. Here’s the bottom line… As we increase the number of explanatory variables in a linear model (e.g. multiple regression) the unadjusted r-squared increaes (green dots) even if the additional explanatory variables contain only random numbers. The adjusted r-squared is “adjusted” so it does not! So if we simply want to know the proportion of variance explained by our model we are fine using the unadjusted r-squared.

Getting lost packages

To use the functions in an add-on package you first need to install the package. Remember you only need install it once. During the writing of the book, and in early 2018 the normal method for installing the ggfortify add-on package didn’t work (we got the message package ggfortify is not available (for R Version 3.2.4)). This has not happened for some time, so hopefully you won’t experience it. If you do…

Importing data update

As the Second Edition of Getting Started with R was going to press, Rstudio changed the function it uses to import data in the Import Dataset tool, from the base function read.csv() to the read_csv() function in the readr package. Since then, the Import Dataset button gives a menu with an option to use either (“base” uses read.csv and “readr” uses read_csv) From the Rstudio Blog about the readr package: