Methods in Experimental Ecology I (PCB 6466): Fall 2023

Course Information
  • Time: Tuesdays & Thursdays  (2:00-3:20)
  • Room: Bio 305
  • Instructor: Dave Jenkins, office = BIO 111B, email [david.jenkins AT ucf.edu] for help / meetings
  • TA: Ashley Reaume office = 133, email [ashley.reaume AT ucf.edu] for help / meetings
  • A resource: Hector, A (2021) The new statistics with R – an introduction for biologists. Oxford.  (Available here Free if logged in UCF network)

Resources

Description

Learn how to design, analyze and interpret experiments and quantitative observations. Introduction to modern statistical software and basic statistical methods needed to collect, organize and interpret data critically. For beginning graduate and senior undergraduate researchers, this course bridges between undergraduate stats and Methods II.

TENTATIVE SCHEDULE (subject to hurricanes, changes in covid policies, etc.)
Week Videos etc. (BEFORE class) Reading (BEFORE class) In-Class Topics Assignments
1:

Aug 22, 24

Installing R & RStudio

RStudio Orientation

swirlstats.com

data carpentry

Plot: generic X-Y Plotting

 

Much ado about p

But stats are > p

 

Course overview & goals

Popularity of stats software

AI & R

Intro to R & RStudio

  1. Install R & RStudio.
  2. Make a plot in R. Any plot.
  3. Email it to Ashley
2:

Aug 29

F’BALL AUG 31

Hypotheses 1 , 2

Chamberlin (1890)

McGill et al. (2006) excerpt

Ecology & strong inference

Chaves (2010)

Buchanan (2019)

Readings discussion

Homework #1

(Due 5 Sep)

3:

Sep 5, 7

Data basics

Handling data

dplyr lesson 1

dplyr lesson 2

Experimental Designs 1

Experimental Designs 2

Many Choices

Helicopter experiment

 

Handling Data #1

Handling Data #2

helicopter data.csv

helicopter data.xls

Homework #2

(Due 12 Sep)

4:

Sep 12, 14

How To Graph in RStudio: The Basics

ggplot 2 Lecture 1 & Lecture 2

Graphing in R ggplot2 #1 & #2

Tufte in R

Getting Started with Charts in R

Plot: generic X-Y Plotting

R cheat sheets (!) including ggplot

lattice

Graphing I (as.txt)

Graphing II (as .txt)

Homework #3

Silwood weather data (.txt)

Silwood weather data (.csv)

(Due 19 Sep)

5:

Sep 19, 21

Probabilities

Distributions

Normality tests I

Normality tests II

Homogeneity tests

Do not log-transform count data

Normality & Variance

Transforming Data (new)

Homework #4

species pH data

(Due 26 Sep)

6:

Sep 26, 28

Z- and t-tests

ANOVAs I & II

OLS Regressions

 

t tests

NC births data

Copter Analyses I

Homework #5

zinc data

barley data

possum data

(Due 3 Oct)

7:

Oct 3, 5

Model selection (w/ AIC) Anderson et al. (2000)

Anderson & Burnham (2002)

Readings discussion

Copter Analyses II

Using AIC (new! improved!)

Homework #6

MLBbattingdata2022

(Due 10 Oct)

8:

Oct 10, 12

Representing statistical variation

Min. N for regressions

CIs, not posthoc power!

CIs

CIs.R.txt

Power analysis

Homework #7

chickwts ipomopsis

(Due 17 Oct)

9:

Oct 17, 19

 

SMA Regressions

ANCOVAs

Warton et al. (2012) Linear & SMA Regressions

ANCOVAs

tancat   FLHg

Homework #8

fishery

zebrafish

(Due 24 Oct)

10:

Oct 24, 26

Multiple Regressions Multiple Regressions I

Multiple Regressions II

streams.csv

Regression Outputs & Residuals

Homework #9

timber2.txt

(Due 31 Oct)

11:

Oct 31, Nov 2

Generalized Linear Models I

Generalized Linear Models II

GLMs I

beetlemeans.csv

GLMs II (& CART)

ozone data

Homework #10

 

(Due 7 Nov)

12:

Nov 7, 9

 

Intro to Mixed Effects Models

Mixed Effect ANOVAs

plantdata0615

Mixed Effect ANOVAs II

beetlesdata.csv

Homework #11

carrots

(Due 14 Nov)

13:

Nov 14, 16

 

Logistic Regressions

 

Plotting complex models

Mixed Effects Regressions

Seals data

Logistic Regressions

islandbird

Homework #12

parasites

(Due 28 Nov)

14:

Nov 21

T’GIVING

Intro to Multivariate Analyses

Ordinations

NMDS in R

ordinations.R (as txt)

diplo2017

Ohyama et al. (2018)

– – – –
15:

Nov 28, 30

– – – –

– – – – practice 1

Dave’s attempt (txt)

sulphur dioxide data (txt)

Final Exam to You Nov 30

final exam

corrected censusdata.txt

FLBearHunt.csv

asparagus.txt

16:

Dec 5, 7

Finals Week

Finals Week  Finals Week

Final DUE THURS DEC 7