Preface, data sets, and past exams

This eBook contains all of the lecture notes and lab exercises that we will do this semester in Biometry. While I have made every effort to cite sources where I’ve used “found” material, this eBook reflects my own personal notes drawn up over nearly a decade of work and some material may not properly identify the original sources used in drawing up my initial lecture notes. As I have moved this material into an online eBook, I have tried to better document material inspired by or drawn from other sources. If you find anything in these notes that is not properly cited or sourced, please let me know so it can be amended. Any mistakes are mine and mine alone.

Data sets

Here are the datasets used in this course. You can download the data set from the course GitHub page and then save it to your local directory. To do that, right-click or control-click on the “raw” button; this will allow you to download the file in its original format.

The dataset links take you here. The "raw" button allows you to download the file

Figure 0.1: The dataset links take you here. The “raw” button allows you to download the file

Another way to do it is to use the ‘readr’ package, as I demonstrate here for the clouds.csv dataset:

library(readr)
clouds <- read_csv("https://raw.githubusercontent.com/hlynch/Biometry2024/master/_data/clouds.csv")
  • clouds (csv): link [1]
  • clouds (txt): link [1]
  • Prestige: link [2]
  • skulls: link [3]
  • diabetes: link [4]
  • WaterData: link [5]
  • FoxFurProduction: link [6]
  • fish: link [7]
  • Week-9-Data: link [8]
  • bomregions2012: link [9]
  • Challenger_data: link [10]
  • Brogan_et_al_2013_Fig1Data: link [11]
  • fruit_flies: link [12]
  • medley: link [13]
  • quinn: link [14]
  • TwoWayANOVAdata_balanced: link [15]
  • TwoWayANOVAdata: link [16]
  • TwoWayANOVAdata: link [17]
  • flatworms: link [18]
  • flies: link [19]
  • rats: link [20]
  • tobacco: link [21]
  • crabs: link [22]
  • frogs: link [23]
  • MammalLifeHistory: link [24]
  • Historic-lichen_data: link [25]
  • Lichen-sites-area: link [26]
  • Temperature_and_isolation: link [27]
  • lovett2: link [28]

[1] Source: Chambers, Cleveland, Kleiner, and Tukey. (1983). Graphical Methods for Data Analysis. Wadsworth International Group, Belmont, CA, 351. Original Source: Simpson, Alsen, and Eden. (1975). A Bayesian analysis of a multiplicative treatment effect in weather modification. Technometrics 17, 161-166.

[2] Fox, J and Weisberg, HS (2011) An R Companion to Applied Regression. 2nd ed. Thousand Oaks, CA: Sage Publications.

[3] Thomson, A and Randall-Maciver, R (1905) Ancient Races of the Thebaid, Oxford: Oxford University Press. Also found in: Hand, D.J., et al. (1994) A Handbook of Small Data Sets, New York: Chapman & Hall, pp. 299-301. Manly, B.F.J. (1986) Multivariate Statistical Methods, New York: Chapman & Hall.

[4] Willems JP, Saunders JT, DE Hunt, JB Schorling (1997) Prevalence of coronary heart disease risk factors among rural blacks. A community-based study. Southern Medical Journal 90:814-820; and Schorling JB, Roach J, Siegel M, Baturka N, Hunt DE, Guterbock TM, Stewart HL (1997) A trial of church-based smoking cessation interventions for rural African Americans. Preventive Medicine 26:92-101.

[9] ‘DAAG’ R package

[10] Siddhartha, RD, Fowlkes, EB, and Hoadley, B (1989) Risk analysis of the space shuttle: Pre-Challenger prediction of failure. Journal of the American Statistical Association 84: 945-957.

[11] Brogan, WR III, and Relyea, RA (2013) Mitigation of Malathion’s acute toxicity by four submersed macrophyte species. Environmental toxicology and Chemistry 32(7): 1535-1543.

[13] Quinn G, and Keough, M. Experimental Design & Data Analysis for Biologists. (2002) Cambridge University Press, UK.

[14] Quinn G, and Keough, M. Experimental Design & Data Analysis for Biologists. (2002) Cambridge University Press, UK.

[23] Hunter, D (2000) The conservation and demography of the southern corroboree frog (Pseudophryne corroboree). M.Sc. thesis, University of Canberra, Canberra.

[24] Morgan Ernest SK (2003) Life history characteristics of placental non-volant mammals. Ecology 84: 3402.

[25] Lynch, HJ Personal data.

[26] Lynch, HJ Personal data.

[27] Lynch, HJ Personal data.

[28] Lovett, GM, Weathers, KC, and Sobczak, WV (2000) Nitrogen saturation and retention in forested watersheds of the Catskill Mountains, New York. Ecological Applications 10(1): 73-84.

Exams

In an effort to provide as much transparency as possible on the scope and style of exams, I have made all previous exams available below. Keep in mind that Biometry has developed and changed over the 10+ years I have been teaching it. There are topics we used to cover that we no longer cover, and there are topics we cover now that were not always included as part of the syllabus. Some of the questions used in previous exams are now being used in problem sets. Exams are largely written anew each year but some questions get re-used and some of these questions may appear in future exams. Note that I was on sabbatical in 2019 and there are no exams provided for that year.

Midterms

  • Spring 2012 Midterm: link
  • Spring 2013 Midterm: link
  • Spring 2014 Midterm: link
  • Spring 2015 Midterm: link
  • Spring 2016 Midterm: link
  • Spring 2017 Midterm: link
  • Spring 2018 Midterm: link
  • Spring 2020 Midterm: link
  • Spring 2021 Midterm: link
  • Spring 2022 Midterm: link
  • Spring 2023 Midterm: link

Finals

  • Spring 2012 Final: link
  • Spring 2013 Final: link
  • Spring 2014 Final: link
  • Spring 2015 Final: link
  • Spring 2016 Final: link
  • Spring 2017 Final: link
  • Spring 2018 Final: link [See note below]
  • Spring 2020 Final: link
  • Spring 2021 Final: link
  • Spring 2022 Final: link [See note below]
  • Spring 2023 Final: link

Note that there are some questions that are poorly worded or confusing.

Spring 2018 Final 10c and 10d are ill posed and should be ignored.

Spring 2022 Final question 5 should have been written as

\[ Y_{i} \sim N(\beta_{0}+\beta_{1}SST_{i}+\beta_{2}PreyDensity_{i}+ \\ \beta_{3}StartingLength_{i}+\beta_{4}I[Group_{i}==\mbox{Adult Female}]+\beta_{5}I[Group_{i}==\mbox{Juvenile Male}]+\\ \beta_{6}I[Group_{i}==\mbox{Juvenile Female}],\sigma^{2}) \]

Helpful RMarkdown resources

Biometry students throughout the years have discovered various helpful tools, which I share here. No endorsement of these tools is implied, and their functionality and existence on the web is subject to change at any time.

  • Making pretty tables*

TableConvert How to make beautiful tables in R (blog post)