# Methods

### Introduction to Bayesian Methods guest lecture

October 18, 2012 |

This is a talk I gave this week in Advanced Biostatistics at McGill. The goal was to provide an gentle introduction to Bayesian methodology and to demonstrate how it is used for inference and prediction. There is a link to an accompanying R script in the slides [Read more...]

### An Improvement to Coefficient Plots

July 3, 2012 |

I recently posted about coefficient plots, discussing my approach and providing some example R code to create the graphs. I had the good fortune of hearing Amanda Driscoll give a talk recently, and she made a small, but really nice … Continue rea... [Read more...]

### Coefficient Plots in R

June 30, 2012 |

One popular trend in presenting results is the "coefficient plot," an alternative to the table of regression coefficients. I am seeing this a little more often in political science research and have received a few requests for code, so I … Contin... [Read more...]

### Why You Shouldn’t Conclude "No Effect" from Statistically Insignificant Slopes

June 16, 2012 |

It is quite common in political science for researchers to run statistical models, find that a coefficient for a variable is not statistically significant, and then claim that the variable "has no effect." This is equivalent to proposing a research &#8... [Read more...]

### Multiply Imputing an Outcome Variable

October 12, 2011 |

Some scholars suggest that multiply imputing an outcome variable is incorrect. I use intuition and simulation to argue that multiply imputing outcomes can drastically improve estimates, even in the case of non-ignorable missingness. Continue reading &#... [Read more...]

### My take on an R introduction talk

September 9, 2011 |

Here is a short intro R talk I gave today...for what it's worth...R Introduction View more presentations from schamber

### R Code for Bow Tie Plots

August 22, 2011 |

Earlier, I discussed the nice properties of bow tie plots for visualizing and understanding inferences from simple randomized treatment experimental designs. R code to quickly create these plots is available here. You can use the command source("htt... [Read more...]

### iEvoBio 2011 Synopsis

June 22, 2011 |

We just wrapped up the 2011 iEvoBio meeting. It was awesome! If you didn't go this year or last year, definitely think about going next year.Here is a list of the cool projects that were discussed at the meeting (apologies if I left some out):Vistrails...

### How to fit power laws

June 7, 2011 |

A new paper out in Ecology by Xiao and colleagues (in press, here) compares the use of log-transformation to non-linear regression for analyzing power-laws.They suggest that the error distribution should determine which method performs better. When you...

### Phylometa from R: Randomization via Tip Shuffle

April 16, 2011 |

I wrote earlier about some code I wrote for running Phylometa (software to do phylogenetic meta-analysis) from R.I have been concerned about what exactly is the right penalty for including phylogeny in a meta-analysis. E.g.: AIC is calculated from Q in...

### Adjust branch lengths with node ages: comparison of two methods

April 10, 2011 |

Here is an approach for comparing two methods of adjusting branch lengths on trees: bladj in the program Phylocom and a fxn written by Gene Hunt at the Smithsonian.Get the code and example files here: http://wp.me/PRT1F-2vGet phylocom here: http:/...

### Five ways to visualize your pairwise comparisons

March 5, 2011 |

In data analysis it is often nice to look at all pairwise combinations of continuous variables in scatterplots. Up until recently, I have used the function splom in the package lattice, but ggplot2 has superior aesthetics, I think anyway.Here a fe... [Read more...]

### Phenotypic selection analysis in R

February 24, 2011 |

I have up to recently always done my phenotypic selection analyses in SAS. I finally got some code I think works to do everything SAS would do. Feedback much appreciated!########################Selection analyses#############################install.pac...