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<!DOCTYPE html>
<html>
<head>
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<title>Course Schedule and Readings</title>
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<li>
<a href="index.html">Home</a>
</li>
<li>
<a href="overview.html">Overview</a>
</li>
<li>
<a href="schedule.html">Schedule</a>
</li>
<li>
<a href="texts.html">Texts</a>
</li>
<li>
<a href="final.html">Final Project</a>
</li>
<li>
<a href="extra.html">Going Beyond</a>
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<li>
<a href="https://docs.google.com/document/d/1fyRqpWrM8dS1y1VxVVhs0cLlpHQCGbRR48Lzy9OI-r8/edit?usp=sharing">Syllabus</a>
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<div id="header">
<h1 class="title toc-ignore">Course Schedule and Readings</h1>
</div>
<!--
NEXT TIME I TEACH 607 in 2024
redo explaining least squares - it's not good in the lecture
re-arrange the linear regression lab
- workflow
- transforms
- viz of prediction intervals and such
Causal Intro is 2 lectures
- End is week and flabby. Rework
Add more on randomization (dee slides) and SUTVA for expts
- It's really 2 lectures
-->
<p>While the topics covered are broad, each week will feature different
examples from genetics, ecology, molecular, and evolutionary biology
highlighting uses of each individual set of techniques.</p>
<p>F = Fieberg, R4DS = <a href="https://r4ds.hadley.nz/">Wickham et
al.</a>, U/P for linked pdfs = biol607</p>
<p>Change .html to .Rmd in your browser to get the markdown of all
lectures, etc.</p>
<p><strong>Recorded Lecture</strong>: All lectures and labs will be
recorded and are available at <a
href="https://www.youtube.com/playlist?list=PLZRMqMK8aRmIMuiEX-QVxLNk2o6SlRa-m"
class="uri">https://www.youtube.com/playlist?list=PLZRMqMK8aRmIMuiEX-QVxLNk2o6SlRa-m</a></p>
<p><strong>Turning in Homework</strong>: All homework should be
completed using RMarkdown or Quarto. You’ll freely mix answers in text
and code there. Use projects. Please zip up the full project folder for
each to submit so that we have the .rmd (or .qmd), .html output, data,
etc. and can recompile your homework if we need to. An ideal project
structure would be something like this:</p>
<p>homework_X/<br />
|— markdown<br />
|— scripts<br />
|— data</p>
<p>directory structure, so that all data is in <code>data/</code>.
<strong>Please zip up the archive for the homework and standardize
filenames as follows:
<code>number_lastName_firstName_2023.zip</code></strong> where number is
the week number the homework is due (from weeks below) and make sure to
include the 0s for numbers like 01), and your last and first names -
well, you should know them!</p>
<p>To submit homework, use the dropbox link you were sent by the TA.</p>
<div id="block-1-introduction-to-programming-and-reproducibility"
class="section level2">
<h2>Block 1: Introduction to Programming and Reproducibility</h2>
<div id="week-1." class="section level3">
<h3>Week 1.</h3>
<p>9/4/2023<br />
<strong>Lecture:</strong> <a href="lectures/01_intro_x.html">Class
intro</a>, <a href="lectures/02_r_intro.html">Intro to R</a>.<br />
<strong>Lab:</strong> <a
href="lectures/02a_r_intro_list_matrix_df.html">Matrices, Lists and Data
Frames</a>. <a
href="https://rmarkdown.rstudio.com/lesson-1.html">Introduction to
Markdown</a><br />
<strong>Reading:</strong> R4DS <a
href="https://r4ds.hadley.nz/intro">Intro</a>, <a
href="https://r4ds.hadley.nz/workflow-basics">Workflow basics</a>, <a
href="https://r4ds.hadley.nz/workflow-scripts">Scripts and Projects</a>,
<a href="https://r4ds.hadley.nz/workflow-style">Code Style</a>, <a
href="http://r4ds.had.co.nz/vectors.html">Vectors</a>, and <a
href="https://r4ds.hadley.nz/quarto">Quarto</a><br />
<strong>Further Exploration:</strong> <a
href="https://r4ds.hadley.nz/quarto-formats">Quarto Formats</a>, <a
href="https://quarto.org/" class="uri">https://quarto.org/</a> for
everything!<br />
<strong>Cheat Sheets:</strong> <a
href="https://rstudio.github.io/cheatsheets/quarto.pdf">Quarto Cheat
Sheet</a><br />
<strong>Install R:</strong> Go to <a href="https://cloud.r-project.org/"
class="uri">https://cloud.r-project.org/</a> and get the right version
of R for you. Then, go to <a
href="https://www.rstudio.com/products/rstudio/download/#download"
class="uri">https://www.rstudio.com/products/rstudio/download/#download</a>
and install Rstudio.<br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-intro-2023"
class="uri">https://etherpad.wikimedia.org/p/607-intro-2023</a><br />
<strong>Homework:</strong> <a href="./homework/intro_to_r.html">Intro to
R and Data Frames</a></p>
</div>
<div id="week-2." class="section level3">
<h3>Week 2.</h3>
<p>9/11/2023<br />
<strong>Lecture:</strong> <a
href="lectures/05_data_viz_principles.pptx">Data visualization</a><br />
<strong>Lab Topic:</strong> <a
href="lab/04_ggplot_palmer_intro.html">Introduction to
ggplot2</a>.<br />
<strong>Reading:</strong> R4DS Chapters on <a
href="https://r4ds.hadley.nz/data-visualize">Data Vizualization</a>, <a
href="https://r4ds.hadley.nz/layers">Layers of Plots</a>, and <a
href="https://r4ds.hadley.nz/communication">Graphics for
Communication</a>, <a
href="https://journal.r-project.org/articles/RJ-2022-020/">Introducing
Palmer Penguins</a><br />
<strong>Further Exploration:</strong> <a
href="http://byrneslab.net/classes/biol607/readings/Friendly_2008_dataviz_history.pdf">Friendly
2008 on History of Data Viz</a>, <a
href="http://byrneslab.net/classes/biol607/readings/Unwin_2008_dataviz.pdf">Unwin
2008</a>, <a
href="http://www.datacarpentry.org/R-ecology-lesson/02-starting-with-data.html">DC
Starting with Data</a>, <a
href="https://serialmentor.com/dataviz/">Fundamentals of Data
Visualization</a> - note, this is a whole book, but scan it - it’s
amazing<br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/dataviz-2023"
class="uri">https://etherpad.wikimedia.org/p/dataviz-2023</a><br />
<strong>Packages used this Week:</strong> <a
href="https://ggplot2.tidyverse.org/">ggplot2</a>, <a
href="https://cran.r-project.org/web/packages/ggridges/vignettes/introduction.html">ggridges</a>,
<a href="https://mjskay.github.io/ggdist/">ggdist</a> -
<code>install.packages(c("ggplot2", "ggridges", "palmerpenguins", "ggdist"))</code><br />
<strong>Cheat Sheets:</strong> <a
href="https://posit.co/wp-content/uploads/2022/10/data-visualization-1.pdf">Ggplot2
cheat sheet</a>, <a
href="https://biol355.github.io/Readings/choosing-a-good-chart-09.pdf">Choosing
a good chart cheat sheet</a><br />
<strong>Homework:</strong> <a href="./homework/ggplot.html">ggplot2
homework</a></p>
</div>
<div id="week-3." class="section level3">
<h3>Week 3.</h3>
<p>9/18/2023<br />
<strong>Lecture/Lab:</strong> <a
href="https://datacarpentry.org/R-ecology-lesson/02-starting-with-data.html">Data
import, using libraries</a>, <a
href="https://datacarpentry.org/R-ecology-lesson/03-dplyr.html">Pipes,
data manipulation, summarization, and making it tidy</a><br />
<!--, [Joins](lectures/18_join.html) --> <strong>Data:</strong> <a
href="https://ndownloader.figshare.com/files/2292169">Portal Data</a> -
and learn more <a href="https://portal.weecology.org/">here</a><br />
<strong>Reading:</strong> <a
href="./readings/Browman_and_Woo_Spreadsheets.pdf">Data organization in
spreadsheets</a>, R4DS Chapters on <a
href="https://r4ds.hadley.nz/spreadsheets">data import</a>, <a
href="https://r4ds.hadley.nz/workflow-style.html#sec-pipes">pipes</a>,
<a href="https://r4ds.hadley.nz/data-transform.html">data
transformation</a>, <a href="https://r4ds.hadley.nz/data-tidy.html">tidy
data</a><br />
<strong>Optional Reading:</strong> <a
href="https://dynamicecology.wordpress.com/2016/08/22/ten-commandments-for-good-data-management/">10
Commandments for Good Data Managament</a>, <a
href="https://bookdown.org/rdpeng/exdata/managing-data-frames-with-the-dplyr-package.html">Managing
Data Frames with the Dplyr package</a>, <a
href="http://r4ds.had.co.nz/strings.html">Strings</a>, <a
href="https://r4ds.hadley.nz/factors.html">factors</a>, and <a
href="http://r4ds.had.co.nz/dates-and-times.html">Dates</a><br />
<strong>Cheat Sheets:</strong> <a
href="https://rstudio.github.io/cheatsheets/data-import.pdf">Reading
data into R</a>, <a
href="https://rstudio.github.io/cheatsheets/data-transformation.pdf">Dplyr
cheat sheet</a>.<br />
<strong>Packages:</strong>
<code>install.packages(c("dplyr", "janitor", "skimr", "lubridate", "tidyr", "readr", "readxl", "tibble"))</code>
- <a href="https://readr.tidyverse.org/">readr</a>, <a
href="https://readxl.tidyverse.org/">readxl</a>, <a
href="https://tibble.tidyverse.org/">tibble</a>, <a
href="https://docs.ropensci.org/skimr/">skimr</a>, <a
href="https://garthtarr.github.io/meatR/janitor.html">janitor</a>, <a
href="https://docs.ropensci.org/visdat/">visdat</a><br />
<strong>Etherpad:</strong> <a
href="http://etherpad.wikimedia.org/p/607-tidy-2023"
class="uri">http://etherpad.wikimedia.org/p/607-tidy-2023</a><br />
<strong>Homework:</strong> <a href="./homework/dplyr_tidyr.html">Data
Manipulation and Pivot homework</a></p>
</div>
<div id="week-4." class="section level3">
<h3>Week 4.</h3>
<p>9/25/2023<br />
<strong>Lecture:</strong> <a
href="lectures/03_sampling_lecture_x.html">What is a Sample?</a> and <a
href="lectures/04_sampling_dist.html">Sampling Distribution</a>.<br />
<strong>Lab Topic:</strong> <a
href="lab/sample_distributions_simulation.html">Sampling and
simulation</a>.<br />
<strong>Reading:</strong> <a
href="http://byrneslab.net/classes/biol607/readings/Cumming_2007_error.pdf">Cumming
et al. 2007 on SDs, SEs, and CIs</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/sampling-2023"
class="uri">https://etherpad.wikimedia.org/p/sampling-2023</a><br />
<strong>Packages for the Week:</strong> <a
href="https://dplyr.tidyverse.org/">dplyr</a> -
<code>install.packages(c("dplyr", "purrr"))</code><br />
<strong>Homework:</strong> <a
href="./homework/sampling_dist_tidytuesday.html">Sampling, Simulation,
and Tidy Tuesday</a></p>
</div>
</div>
<div id="block-2-linear-models-for-data-analysis"
class="section level2">
<h2>Block 2: Linear Models for Data Analysis</h2>
<div id="week-5." class="section level3">
<h3>Week 5.</h3>
<p>10/2/2023<br />
<strong>Lecture:</strong> Introduction to Regression: <a
href="lectures/linear_regression.html">Correlation and Regression</a>,
<a href="lectures/linear_regression_details.html">Fit and
Precision</a><br />
<strong>Lab Topic:</strong> <a href="lab/06_lm.html">Linear regression,
diagnostics, visualization</a>, and <a
href="lab/data_06.zip">data</a><br />
<strong>Reading:</strong> <a
href="https://fw8051statistics4ecologists.netlify.app/linreg.html">Fieberg
linear regression review</a>, R4DS on <a
href="http://r4ds.had.co.nz/model-basics.html">model basics</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-lm-2023"
class="uri">https://etherpad.wikimedia.org/p/607-lm-2023</a><br />
<!--__In Class Code:__ [reproducible examples](in_class_code/2020/scripts/reprex.R), [lm](in_class_code/2020/scripts/linear_regression.R) -->
<strong>Homework:</strong> <a
href="homework/06_correlation_regression.html">Correlation and Linear
Models</a></p>
</div>
<div id="week-6" class="section level3">
<h3>Week 6</h3>
<p>10/9/2023<br />
<strong>Lecture:</strong> <a href="./lectures/mlr.html">Many
Predictors</a>, <a
href="lectures/categorical_predictors.html">Categorical Predictors: Just
Another Linear Model</a><br />
<strong>Lab Topic:</strong> <a
href="lab/multiple_predictors.html">Models with Categorical
Variables</a><br />
<strong>Lab Data:</strong> <a
href="lab/data/categorical_data.zip">Multiple Files</a><br />
<strong>Reading:</strong> <a
href="https://fw8051statistics4ecologists.netlify.app/matrixreg">Feiberg
3</a>, <a href="https://lindeloev.github.io/tests-as-linear/">Common
statistical tests are linear models</a>, <a
href="https://fw8051statistics4ecologists.netlify.app/multicol.html">Feiberg
ch 6</a><br />
<strong>Optional Reading:</strong> <a
href="./readings/Hector_et_al-2010-Journal_of_Animal_Ecology.pdf">Analysis
of variance with unbalanced data: an update for ecology &
evolution</a>, <a href="https://www.jstor.org/stable/1943075">Day and
Quinn 1989 on Post-hocs</a>.<br />
<strong>Packages for The Week:</strong>
<code>install.packages(c("car", "emmeans", "multcompView", "contrast", "visreg"))</code><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-many-predictors-2023"
class="uri">https://etherpad.wikimedia.org/p/607-many-predictors-2023</a><br />
<strong>Homework:</strong> None. Catch up!</p>
<!-- __In Class Code:__ [comparing two means](./in_class_code/2020/scripts/comparing_means.R) -->
</div>
<div id="week-7" class="section level3">
<h3>Week 7</h3>
<p>10/16/2023<br />
<strong>Lectures:</strong> <a
href="./lectures/many_types_of_predictors.html">Many categories or
mixing categories and continuous predictors</a>, <a
href="lectures/interactions_lm.html">When one predictor’s effect depends
on the other</a><br />
<strong>Lab Topic:</strong> <a
href="lab/complex_linear_models.html">Models with many types of
predictors - and interactions!</a><br />
<strong>Lab Data:</strong> <a href="lab/data_10.zip">Multiple
Files</a><br />
<strong>Reading:</strong> <a
href="https://fw8051statistics4ecologists.netlify.app/multicol.html">Feiberg
ch 6</a>, <a href="./readings/Schielzeth_2010_MEE.pdf">Simple means to
improve the interpretability of regression coefficients</a>, <a
href="https://onlinelibrary.wiley.com/doi/full/10.1111/brv.12939">Understanding
‘it depends’ in ecology: a guide to hypothesising, visualising and
interpreting statistical interactions</a><br />
<strong>Optional Readings:</strong> <a
href="https://besjournals.onlinelibrary.wiley.com/doi/full/10.1111/2041-210X.13714">Interactions
in statistical models: Three things to know</a>, <a
href="./readings/kramer_blasey_centering.pdf">Centring in regression
analyses: a strategy to prevent errors in statistical
inference</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-complex-linear-models-2023"
class="uri">https://etherpad.wikimedia.org/p/607-complex-linear-models-2023</a><br />
<strong>Homework:</strong> <a
href="homework/complex_linear_models.html">Complex linear
models</a><br />
<strong>Project Proposal:</strong> <a
href="project_proposal.html">general instructions here</a></p>
</div>
<div id="week-8" class="section level3">
<h3>Week 8</h3>
<p>10/23/2023<br />
<strong>Lecture:</strong> <a
href="lectures/generalized_linear_models.html">Generalized Linear
Models</a>, <a href="lectures/glm_overdispersion.html">Fitting, Count
Data, and Overdispersion</a><br />
<strong>Data:</strong> <a href="./lectures/data/gls/gls_data.zip">GLS
Data</a>, <a href="./lab/gzlm_data.zip">GLM Data</a><br />
<strong>Lab Topic:</strong> <a href="./lab/12_gzlm.html">Generalized
Linear Models</a><br />
<strong>Packages for the Week:</strong>
<code>install.packages(c("MASS", "readxl", "betareg", "DHARMa", "TMB", "glmmTMB"))</code><br />
<strong>Reading:</strong> <a
href="https://fw8051statistics4ecologists.netlify.app/glm.html">Feiberg
on Generalized Linear Models</a>, <a
href="https://fw8051statistics4ecologists.netlify.app/poissonr">Models
for Count Data</a>, <a
href="https://fw8051statistics4ecologists.netlify.app/logistic">Feiberg
on Logistic Regression</a> - ignore Bayes parts in these. <a
href="https://cran.r-project.org/web/packages/DHARMa/vignettes/DHARMa.html">Hartig
DHARMa vignette</a>, <a
href="https://besjournals.onlinelibrary.wiley.com/doi/10.1111/2041-210X.13234">Analyzing
% Cover and Porportional Data</a><br />
<strong>Additional Reading:</strong> <a
href="https://fw8051statistics4ecologists.netlify.app/mle">Maximum
Likelihood</a>, <a
href="http://byrneslab.net/classes/biol607/readings/o'hara_and_kotze_do_not_log_transform.pdf">O’Hara
and Kotze 2010</a>, <a
href="http://byrneslab.net/classes/biol607/readings/Wharton_Hui_2011_Ecology.pdf">Wharton
and Hui 2011</a>, <a
href="https://esajournals.onlinelibrary.wiley.com/doi/full/10.1890/07-0043.1">Ver
Hoef and Boveng 2007 on NB v. Quasi</a>, <a
href="https://rpubs.com/nicoleknight/936037">Intro to Beta Regression
for % Cover Data</a>, <a
href="https://journal.r-project.org/archive/2015/RJ-2015-019/index.html">Zero-One
Inflated Beta Regression</a>, <a
href="https://fw8051statistics4ecologists.netlify.app/gls.html">Feiberg
on GLS</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-glm-2023"
class="uri">https://etherpad.wikimedia.org/p/607-glm-2023</a><br />
<strong>Homework:</strong> <a
href="homework/generalized_linear_model.html">Surviving the
Titanic</a></p>
</div>
<div id="week-9" class="section level3">
<h3>Week 9</h3>
<p>10/30/2023<br />
<strong>Lecture:</strong> <a
href="https://biol609.github.io/lectures/07_random_effects.html#/section">Random
Effects</a>, <a href="lectures/mixed_models.html">Mixed Models</a><br />
<strong>Data:</strong> TBA<br />
<strong>Lab Topic:</strong> <a href="lab/mixed_models.html">Mixed
Models</a><br />
<strong>Packages for the Week:</strong>
<code>install.packages(c("glmmTMB", "lme4", "merTools", "broom.mixed))</code><br />
<strong>Reading:</strong> <a
href="https://fw8051statistics4ecologists.netlify.app/mixed">Linear
Mixed Effects Models</a>, <a
href="https://fw8051statistics4ecologists.netlify.app/glmm">Generalized
Linear Mixed Effects Models</a><br />
<strong>Additional Reading:</strong> <a
href="https://www.cell.com/trends/ecology-evolution/fulltext/S0169-5347(09)00019-6">Generalized
linear mixed models: a practical guide for ecology and evolution</a>, <a
href="https://byrneslab.net/classes/biol609/gelman_hill_ch_12.pdf">Gelman
and Hill Ch 12</a> login/pass biol609, <a
href="https://byrneslab.net/classes/biol609/Zuur_ch_5.pdf">Zuur
ch. 9</a>. <strong>Your One Stop FAQ:</strong> <a
href="https://bbolker.github.io/mixedmodels-misc/">Your One Stop FAQ:
Ben Bolker’s Mixed Model’s FAQ</a>, <a
href="https://svmiller.com/blog/2018/06/mixed-effects-models-optimizer-checks/">optimizer
tips</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-mixed-2023"
class="uri">https://etherpad.wikimedia.org/p/607-mixed-2023</a></p>
<p><strong>MIDTERM</strong>: Due Tues Nov 17th, 5pm. <a
href="exams/exam_2023.html">Get it here</a></p>
</div>
</div>
<div
id="block-3.-experimental-and-observational-study-design-and-causal-inference"
class="section level2">
<h2>Block 3. Experimental and Observational Study Design and Causal
Inference</h2>
<div id="week-10." class="section level3">
<h3>Week 10.</h3>
<p>11/6/2023<br />
<strong>Lecture:</strong> <a href="lectures/causal_diagrams.pptx">Causal
Inference</a><br />
<strong>Lab:</strong> <a href="lab/dagitty.html">Daggity and Causal
Models</a><br />
<strong>Reading:</strong> <a href="./readings/Arif_et_al_2022.zip">Arif
et al. on Structural Causal Models</a>, <a
href="https://fw8051statistics4ecologists.netlify.app/causal">Fieberg on
Causal Models</a>.<br />
<strong>Optional Reading:</strong> <a
href="https://mixtape.scunning.com/04-potential_outcomes">An Intro to
the PO Framework from The Causal Mixtape</a>, <a
href="Grace_and_Irvine_2019.pdf">Grace and Irvine on designing SCMs</a>,
<a
href="https://pdf.sciencedirectassets.com/271328/1-s2.0-S1047279716X00105/1-s2.0-S1047279716302800/main.pdf">Does
Water Kill?</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-causal-2023"
class="uri">https://etherpad.wikimedia.org/p/607-causal-2023</a></p>
</div>
<div id="week-11." class="section level3">
<h3>Week 11.</h3>
<p>11/13/2023<br />
<strong>Lecture:</strong> <a
href="./lectures/causality_experiments.pptx">Causal Inference and
Experiments</a>, <a href="lectures/causal_observational.pptx">Using
causal models to get valid inference from observational and
quasi-experimental studies</a><br />
<strong>Paper Discussion:</strong> Thursday discussion of <a
href="readings/exp_design_papers.zip">papers</a> - see <a
href="https://docs.google.com/spreadsheets/d/1r0VfnAJ3tuJufnLnrVC6Nx0qiyP4l6QILarKTsduov0/edit?usp=sharing">here</a>
for assignments<br />
<strong>Reading:</strong> <a
href="./readings/Kimmel_et_al_2021.pdf">Kimmel et al. on Experimental
Design</a>, <a href="./readings/McElreath_Ch_6.pdf">The Causal Dag and
Haunted Terror</a>, <a href="readings/butsic_et_al_2017.pdf">Butsic et
al 2021 on Quasi-Experiments</a>,<br />
<strong>Optional Reading:</strong> <a
href="readings/Gotelli&EllisonChapter7.pdf">A Beastiary of
Experimental Designs</a>, <a
href="BellemareBloemWexlerFDCJune2020.pdf">Bellemare et al. on Front
Doors</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-causal-expts-2023"
class="uri">https://etherpad.wikimedia.org/p/607-causal-expts-2023</a></p>
</div>
<div id="week-12." class="section level3">
<h3>Week 12.</h3>
<p>11/20/2023<br />
<strong>Thanksgiving Week</strong>. <strong>Paper Discussion:</strong>
Discussion of <a href="readings/obs_sampling.zip">papers</a> - see <a
href="https://docs.google.com/spreadsheets/d/1r0VfnAJ3tuJufnLnrVC6Nx0qiyP4l6QILarKTsduov0/edit?usp=sharing">here</a>
for assignments<br />
<strong>Optional Reading:</strong> <a
href="readings/griffith_collider_bias_covid.pdf">Collider Bias and
Covid</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-obs-2023"
class="uri">https://etherpad.wikimedia.org/p/607-obs-2023</a></p>
</div>
</div>
<div id="block-4.-drawing-inference-from-studies"
class="section level2">
<h2>Block 4. Drawing Inference from Studies</h2>
<div id="week-13." class="section level3">
<h3>Week 13.</h3>
<p>11/27/2023<br />
<strong>Lecture:</strong> Ways of Knowing: <a
href="./lectures/linear_regression_nht">NHT</a>, <a
href="lectures/freq_testing.html">NHT and testing models</a>, <a
href="./lectures/power_analysis.html">Power Analysis</a><br />
<strong>Lab Topic:</strong> <a href="lab/nht.html">Null Hypothesis
Testing</a>, <a href="lab/power_analysis_tidy.html">Power
Analysis</a><br />
<strong>Data for Lab</strong>: <a
href="lab/data/18e4MoleRatLayabouts.csv">mole rats</a>, <a
href="lab/data/18e3IntertidalAlgae.csv">intertidal algae</a>, <a
href="lab/data/cryptoDATA.csv">cryptosporidium infection</a>, <a
href="lab/data/Keeley_rawdata_select4.csv">Keeley et al. data</a><br />
<strong>Reading:</strong> W&S 20, <a
href="./readings/muff_et_al_2022.pdf">Muff et al. 2022 on p-values</a>,
<a
href="https://fw8051statistics4ecologists.netlify.app/mle.html">Feiberg
on Maximum Likelihood</a><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-nht-eval-2023"
class="uri">https://etherpad.wikimedia.org/p/607-nht-eval-2023</a><br />
<strong>Packages for The Week:</strong>
<code>install.packages(c("car", "MASS", "profileModel"))</code></p>
</div>
<div id="week-14" class="section level3">
<h3>Week 14</h3>
<p>12/4/2023</p>
<p><strong>Lecture:</strong> Ways of Knowing: <a
href="./lectures/crossvalidation.html">Cross-Validation and
AIC</a><br />
<strong>Lab Topic:</strong> <a
href="lab/crossvalidation.html">Cross-Validation and AIC</a><br />
<strong>Reading:</strong> <a
href="https://link.springer.com/article/10.1007/s00265-010-1029-6">AIC
in Behavioral Ecology</a>, <a
href="https://fw8051statistics4ecologists.netlify.app/mmi">Fieberg on
Modeling Strategies</a>, <a
href="./readings/Aho_2014_ecolog_bic.pdf">Aho et al. 2014 on
BIC</a><br />
<strong>Optional Reading:</strong> <a
href="http://byrneslab.net/classes/biol607/readings/Ellison_1996_ecol_app.pdf">Ellison
1996</a><br />
<strong>Optional Books:</strong> <a
href="https://ebookcentral.proquest.com/lib/umboston/reader.action?docID=3035464">Model
Selection and Multimodel Inference</a> <strong>Packages for The
Week:</strong> <code>install.packages(c("AICcmodavg")</code><br />
<strong>Etherpad:</strong> <a
href="https://etherpad.wikimedia.org/p/607-cv-2023"
class="uri">https://etherpad.wikimedia.org/p/607-cv-2023</a></p>
</div>
</div>
<div id="week-15" class="section level2">
<h2>Week 15</h2>
<p>12/11/2023<br />
Project work and Project Presentations on Dec 15th</p>
</div>
</div>
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