Lab 2

Question 1

What does the function setwd() do?

Answer 1

Sets your working directory

Question 2

What command would you enter to set your working directory?

Answer 2

setwd()

Question 3

What does the function read.delim do?

Answer 3

It reads a file that is set up in a matrix where rows represent cases and columns represent variables

Question 4

What would you enter to read a file?

Answer 4

use the read.delim() function, and then use

Question 5

How would you plot a relationship?

Answer 5

Use the plot() function, and enter both variables that you want to look at in the brackets, separated by a comma

Question 6

How would you plot the relationship between two log transformed variables?

Answer 6

You would use the plot() function, and enter the two variables in the brackets, contained in brackets with log10 before them, separated by a comma

Question 7

What would you add to suppress the plotting of the data points?

Answer 7

type=n

Question 8

What would you expect as an output after entering instructions to plot a dataset, and entering type=n?

Answer 8

I would expect a blank plot with space for all data points contained in the specified datasets

Question 9

What does != mean?

Answer 9

It means everything but this

Question 10

What is -999 often?

Answer 10

It is often a placeholder for missing data when a dataset is built

Question 11

What is the formula for average diversification rate?

Answer 11

log(N)/t where N is the extant species richness and t is time

Question 12

What is an OLS?

Answer 12

An Ordinary least-squares is an analysis that fits a model of a relationship between one or more explanatory variables and a continuous variable that minimizes the sum of square errors, where an error is the difference between the actual and the predicted value of the outcome variable

Question 13

What are sum of square errors?

Answer 13

A way to measure the difference between the estimated value based on a certain model and the actual value. A small sum of square error indicates that there is a tight fit between the model and the data

Question 14

How would you fit an OLS regression to a plot?

Answer 14

use test.ols

Question 15

What is the problem with using an OLS regression on phylogenetic data?

Answer 15

OLS regression assumes independence between the data points, but data from a phylogenetic tree are nested in a hierarchical structure with varying degrees of relatedness. It could look like there is a significant line between two variables, when really there are two unrelated groups for example.

Question 16

What is a PGLS?

Answer 16

A Phylogenetic generalized least-squares is a form of regression analysis that estimates the phylogenetic covariances and uses them to modify the parameter estimates of the fitted model.

Question 17

What does the comparative.data function do?

Answer 17

It combines phylogenies with other datasets to ensure consistent structure and ordering for use in functions e.g. remove missing data values and mismatched taxon names between a dataset and a phylogeny

Question 18

How do you fit a PGLS model?

Answer 18

use test.pgls and assign pgls() with your y axis, squigly line and x axis in the brackets. Then enter summary(test.pgls)

Question 19

What p-value is usually considered to be significant?

Answer 19

0.05