Available data files, software and code used in the book

Available data files, software and code used in the book

This page contains datafiles and code used for some of the examples in N.J. Gotelli & A.M. Ellison (2004) A primer of ecological statistics. Sinauer Associates, Sunderland, Massachusetts.

Please let us know if you are using the Primer or these data for teaching purposes!

Errata are also available.

Data are in space-delimited ASCII text, and code is provided either as "script" files (.SSC) that will run in S-Plus for Windows, version 6.1 or ASCII text files that can be imported into and run with WinBUGS version 1.4. The code files (.txt or .ssc) can be opened and read with any text editor (e.g., NotePad, WordPad, Emacs, VI).

The book can be ordered directly from Sinauer Associates.

Update history:

• 28 September 2005 - added Darlingtonia datasets for Chapters 9 and 12; updated Literature Cited (AME).
• 17 January 2006 - added full Littoraria dataset for the discriminant analysis example from Chapter 12 (AME).

Chapter 3

• Tibial spine data (Table 3.1). These are simulated, not actual, data.
• S-Plus script for illustrating the Law of Large Numbers and frequentist confidence intervals. The code is modified from that provided by Blume & Royall (2003). The modifications simply make it "generic"; their published code was specific to their published example.

Chapter 4

• Photosynthetic rates of 15 mangrove leaves. These are part of a larger dataset published by Farnsworth and Ellison (1996).
• Note that the figure in the book and the parameter estimates from the Michaelis-Menten fit to these data are incorrect. See the Errata for corrections.

Chapter 5

• Ant nest data (Table 5.1) used for illustrating simple frequentist, Monte Carlo, and Bayesian one-way ANOVA. These are simulated, not actual, data.
• S-Plus script for the Monte Carlo analysis of the ant nest data. These analyses are illustrated in Tables 5.3-5.6 and Figure 5.3 (superseded by revised/updated R-code, 31 May 2010; see Errata).
• R code for the Monte Carlo analysis of the ant nest data. This code replaces the above S-Plus script (31 May 2010).
• WinBUGS code for the Bayesian analysis of the ant nest data. These analyses are illustrated in Figures 5.6-5.9 and Table 5.7.

Chapter 8

• Morphological measurements of 25 Darlingtonia californica pitchers with three added outliers (Table 8.1). These unpublished data were collected by Aaron Ellison, Rebecca Emerson, and Hedda Steinhoff in July 2000, and should not be used in a publication without permission.
• Plant species richness and island area for 17 Galápagos Islands (Table 8.2), as published in the 1st printing of the Primer. The data provided here were originally published in Preston (1962). We retain the island names given by Preston, but have converted island area from square miles to square kilometers.
• Corrected plant species richness and island area for 17 Galápagos Islands (Table 8.2), as corrected in the 2nd printing of the Primer. The data provided here were originally published in Preston (1962). We retain the island names given by Preston, but have converted island area from square miles to square kilometers. See Errata for additional details on these corrected data.

Chapter 9

• Plant species richness and island area for 17 Galápagos Islands plus the added outlier (used for Figure 9.9). These are the same data used in Chapter 8, with the addition of an artificial outlier in row 16.
• S-Plus script for the Monte Carlo analysis of the slopes of the log-log transformed species-area relationship. The results of this analysis are illustrated in Figure 9.8.
• WinBUGS code for the Bayesian analysis of the Galapagos species-area relationship.
• WingBUGS code for the Bayesian analysis of the Galapagos species-area relationship, using the corrected island area data (see Chapter 8 data).
• Acorn data used to illustrate quantile regression (Figure 9.10). These data were published by Schroeder and Vangilder (1997), and discussed further by Cade et al. (1999). Data were kindly provided by Brian Cade.
• The Darlingtonia data used to illustrate logistic regression (Figure 9.11). These data are part of a larger study published by Dixon et al. (2005).
• Ant species density in forest plots in New England used to illustrate multiple regression and collinearity (Figures 9.12-9.14). The data were published by Gotelli & Ellison (2002).
• The data used for the path analysis (Figure 9.15) are currently being prepared for publication. They will be posted here after the manuscript has been accepted for publication.

Chapter 10

• Growth of mangrove roots with living or artificial sponges, used to illustrate a priori contrasts and a posteriori multiple comparisons among means (Tables 10.12 - 10.15, and Figure 10.5). These data are a subset of a larger dataset published by Ellison et al. (1996).
• Download the complete dataset, from the randomized block design described by Ellison et al. (1996).

Chapter 11

• Frequencies of rare plant populations that are declining or not; invaded or not; protected or not; and ordinal light level at each population. Species identities are not given to protect these plants. The data were published by Farnsworth (2004), and are based on compilations from Conservation and Research Plans developed by the New England Wild Flower Society.

Chapter 12

• Morphology, mass, and nutrient content of Darlingtonia californica, used for multivariate analyses described in Tables 12.1 - 12.3, Tables 12.7 and 12.8, and Figures 12.2, 12.3, 12.5-8. These data are part of a larger dataset described by Ellison and Farnsworth (2005).
• S-Plus script for testing multivariate normality. This code is based on algorithms provided by Doornik and Hansen (1994).
• Although it's not used in the book, Fisher's iris data is a common dataset used for multivariate analyses. Doornik & Hansen (1994) benchmark their test for multivariate normality on a subset of Fisher's iris data - the data for I. setosa. This version of Fisher's iris data was copied from The Data and Story Library. It is also included in the Modern Applied Statistics with S (MASS) library of S-Plus (Venables & Ripley 2002).
• Ant presence-absence data used for Principal Coordinates Analysis, Correspondence Analysis, and non-metric multidimensional scaling (Tables 12.9 - 12.10; Figures 12.9 - 12.12). These data were aggregated from data published by Gotelli and Ellison (2002) and Ellison et al. (2002).
• Snail shell data used for cluster analysis and redundancy analysis
• Reduced dataset (Table 12.11) used for the examples in the book (Table 12.12 - 12.14, Figure 12.13 - 12.16).
• The full dataset that was used by Merkt and Ellison (1998). Thanks to Ontrack Data Recovery, these data were recovered in January 2006 from a tape backup made in 1997. This was a good lesson in the importance of keeping students' lab notebooks and maintaining copies of datasets on paper, and the need for timely transfers of files from obsolete to new media.

[Back to Top]

Literature Cited

1. Blume, J. D., and R. M. Royall. 2003. Illustrating the Law of Large Numbers (and confidence intervals). American Statistician 57: 51-57.
2. Cade, B. S., J. W. Terrell, and R. L. Schroeder. 1999. Estimating effects of limiting factors with regression quantiles. Ecology 80: 311-323.
3. Dixon, P. M., A. M. Ellison, and N. J. Gotelli. 2005. Improving the precision of estimates of the frequency of rare events. Ecology 86: 1114-1123.
4. Doornik, J. A., and H. Hansen. 1994. An omnibus test for univariate and multivariate normality. Working paper, Nuffield College, Oxford University.
5. Ellison, A. M., and E. J. Farnsworth. 2005. The cost of carnivory for Darlingtonia californica (Sarraceniaceae): evidence from relationships among leaf traits. American Journal of Botany 92: 1085-1093.
6. Ellison, A. M., E. J. Farnsworth & N. J. Gotelli. 2002. Ant diversity in pitcher-plant bogs of Massachusetts. Northeastern Naturalist 9: 267-284.
7. Ellison, A. M., E. J. Farnsworth, and R. R. Twilley. 1996. Facultative mutualism between red mangroves and root-fouling sponges in Belizean mangal. Ecology 77: 2431-2444.
8. Farnsworth, E. J. 2004. Patterns of plant invasion at sites with rare plant species throughout New England. Rhodora 106: 97-117.
9. Farnsworth, E. J., and A. M. Ellison. 1996. Sun-shade adaptability of the red mangrove, Rhizophora mangle (Rhizophoraceae): changes through ontogeny at several levels of biological organization. American Journal of Botany 83: 1131-1143.
10. Gotelli, N. J., and A. M. Ellison. 2002. Biogeography at a regional scale: determinants of ant species density in New England bogs and forest. Ecology 83: 1604-1609.
11. Merkt, R. E. & A. M. Ellison. 1998. Geographic and habitat-specific morphological variation of Littoraria (Littorinopsis) angulifera (Lamarck, 1822). Malacologia 40: 279-295.
12. Preston, F. W. 1962. The canonical distribution of commonness and rarity: Part I. Ecology 43: 185-215.
13. Schroeder, R.L., and L.D. Vangilder. 1997. Tests of wildlife habitat models to evaluate oak mast production. Wildlife Society Bulletin 25: 639-646.
14. Venables, W. N., and B. D. Ripley. 2002. Modern applied statistics with S, 4th edition. Springer-Verlag, New York.