Assignment 1

Due Date

Friday, January 20, 2012

Data Source

The data for this assignment is the RIKZ data set, the same data set that was used in class during Lab 1. It is a tab-delimited text file.

Questions

1. Download the vegan package of the CRAN site using the Package > Install package(s) menu selections (Windows) or Package & Data > Package Installer menu choices (Mac OS X). Use the diversity function of the vegan package to calculate Simpson's diversity index for the species abundance counts in the RIKZ data set for each site. Simpson's diversity index reports the probability that two randomly chosen individuals from the site are different species.
2. Determine if the Simpson index varies systematically with NAP and whether the relationship is affected by the week that the sample was collected. Carry out formal tests to justify your answer.
3. Graph your final model from step 2 showing as much detail as you can.

Hints

• Remember that even with vegan installed in your copy of R you still need to enter the command library(vegan) in order to load its functions into memory for use during the current R session.
• The diversity function from vegan expects the data to be organized in the following format: species are the columns and sites are the rows. Enter ?diversity to get help on the syntax for this function. Most of the displayed defaults will work for the RIKZ data. The MARGIN argument acts just like the second argument of the apply function: 1 means calculate the statistic separately by row, 2 means calculate the statistic separately by column.
• Your graph in part 3 should show the raw data as well as the regression model.

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