-
Notifications
You must be signed in to change notification settings - Fork 0
/
IPD-syllabus.tex
282 lines (230 loc) · 12.8 KB
/
IPD-syllabus.tex
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
%% UGA guidelines:
%% https://curriculumsystems.uga.edu/curriculum/courses/syllabus/
\documentclass[12pt]{article}
\usepackage[top=2.5cm,left=2.5cm,right=2.5cm,bottom=2cm]{geometry}
\usepackage[pdftex,hidelinks=true,pdfstartview={Fit}]{hyperref}
\usepackage{parskip}
\usepackage{setspace}
\usepackage{tocloft}
\usepackage{verbatim}
\usepackage{xcolor}
\begin{document}
{\centering
{\Large \sc
% Estimation of Fish and Wildlife \\ Population Parameters \\
Inference for Models of Fish and Wildlife \\ Population Dynamics
}
\vspace{6pt}
WILD(FISH) 8390 \\
Lecture: Tues, Thurs 12:45--2:00 PM, Fall 2024 \\
Room 4-516, Warnell \\
\normalsize
\vspace{12pt}
\begin{tabular}[h!]{lccc}
& \textbf{Instructor} & \hspace{0.01cm} & \textbf{Teaching Assistant} \\
& Dr. Richard Chandler & & Jen Brown \\
Office room: & 3-407 & & 4-219 \\
%Phone: 706-542-5818 & & --- \\
Email: & [email protected] & & [email protected] \\
Office hours: & Thur 2:00--3:00 & & Fri 11:00--1:00 \\
\end{tabular}
}
%\vspace{0.1cm}
\normalsize
\vspace{-2mm}
\section*{\normalsize Course Description}
\vspace{-4mm}
Recently developed statistical tools make it possible to fit models of
population dynamics to field data while accounting for observation
error. This course will explain how to use these tools for statistical
inference and prediction about animal population parameters including
abundance, occupancy, survival, recruitment, and dispersal.
\vspace{-2mm}
\section*{\normalsize Course Objectives and Learning Outcomes}
\vspace{-4mm}
By the end of the course, students will know how to (1) design studies
of wildlife population dynamics, (2) fit statistical
models to data collected in the field, (3) interpret results, and (4)
make predictions useful for informing conservation decisions.
\vspace{-2mm}
\section*{\normalsize Textbooks}
\vspace{-4mm}
\begin{itemize}
\setlength\itemsep{-6pt}
\item (AHM1) K\'ery, M. and J.A. Royle. 2016. Applied Hierarchical Modeling
in Ecology: Analysis of Distribution, Abundance and Species Richness
in R and BUGS : Volume 1: Prelude and Static Models. Academic Press.
\href{https://www.sciencedirect.com/book/9780128013786/applied-hierarchical-modeling-in-ecology}{\textcolor{blue}{eBook}}.
\item (AHM2) K\'ery, M. and J.A. Royle. 2020. Applied Hierarchical Modeling
in Ecology: Analysis of Distribution, Abundance and Species Richness
in R and BUGS : Volume 2: Dynamic and Advanced Models. Academic Press.
\href{https://www.sciencedirect.com/book/9780128237687/applied-hierarchical-modeling-in-ecology-analysis-of-distribution-abundance-and-species-richness-in-r-and-bugs}{\textcolor{blue}{eBook}}.
\item (SCR) Royle, J.A., R.B. Chandler, R. Sollmann, and
B. Gardner. 2013. Spatial Capture-Recapture. Academic Press.
Download chapters of the eBook from the UGA library
\href{https://www-sciencedirect-com.proxy-remote.galib.uga.edu/book/9780124059399/spatial-capture-recapture}{\textcolor{blue}{eBook}}.
\end{itemize}
\vspace{-2mm}
\section*{\normalsize Grading}
\vspace{-4mm}
\begin{center}
% \small
\begin{tabular}[h!]{lrr}
\hline
& Quantity & Grade percentage \\
\hline
Weekly assignments$^*$ & 15 & 45\% \\
Final presentation & 1 & 20\% \\
Final paper$^{*}$ & 1 & 30\% \\
Class participation & & 5\% \\
\hline
\end{tabular} \\
\small
\hspace{0mm} $^*$Late assignments will be penalized 3 points/day, up to a maximum of 50 points off. \\
\end{center}
The plus/minus grading system will be used, according to UGA policy,
and assigned following this plus/minus grading scale: A = $>$93-100,
A- = $>$90-93, B+ = $>$87-90, B = $>$83-87, B- = $>$80-83, C+ = $>$77-80,
C = $>$73-77, C-= $>$70-73, D = 60-70, F = $<$60.
\vspace{-2mm}
\section*{\normalsize Attendance}
\vspace{-4mm}
Attendance is optional, but it will be difficult to succeed if you don't participate in lectures.
\vspace{-2mm}
\section*{\normalsize Academic Honesty}
\vspace{-4mm}
As a University of Georgia student, you have agreed to abide by the
UGA academic honesty policy. UGA Student Honor code: ``I will be
academically honest in all of my academic work and will not tolerate
academic dishonesty of others''. A Culture of Honesty, the University's
policy and procedures for handling cases of suspected dishonesty, can
be found at \href{https://honesty.uga.edu/}{here}. You are responsible for
informing yourself about the university’s standards before performing
any academic work. Lack of knowledge of the academic honesty policy is
not a reasonable explanation for a violation. Please ask if you have
questions related to course assignments and the academic honesty
policy. Any form of possible academic dishonesty will be reported to
the UGA Office of the Vice President for Instruction.
\vspace{-2mm}
\section*{\normalsize Academic Coaching}
\vspace{-4mm}
Assistance with time management, test and performance anxiety,
notetaking, motivation, text comprehension, test preparation, and
other barriers to success at
UGA. \href{https://dae.uga.edu/services/academic-coaching/}{\color{blue}
Link} for the Office of Academic Enhancement.
\vspace{-2mm}
\section*{\normalsize Accommodations for Disabilities}
\vspace{-4mm}
If you require a disability-required accommodation, it is essential
that you register with the \href{https://drc.uga.edu}{Disability Resource Center} (Clark Howell
Hall; 706-542-8719)
and notify me of your eligibility for reasonable accommodations. We
can then plan how best to coordinate your accommodations. Please note
that accommodations cannot be provided retroactively.
\vspace{-2mm}
\section*{\normalsize Mental Health and Wellness Resources}
\vspace{-4mm}
\begin{itemize}
\setlength\itemsep{-6pt}
\item If you or someone you know needs assistance, you are
encouraged to contact Student Care and Outreach in the Division of
Student Affairs at 706-542-7774 or visit
\href{https://sco.uga.edu}{their website}. They
will help you navigate any difficult circumstances you may be facing
by connecting you with the appropriate resources or services.
\item UGA has several resources for a student seeking mental health
\href{https://www.uhs.uga.edu/bewelluga/bewelluga}{services} or
\href{https://www.uhs.uga.edu/info/emergencies}{crisis support}.
\item If you need help managing stress anxiety, relationships, etc.,
please visit \href{https://www.uhs.uga.edu/bewelluga/bewelluga}{BeWellUGA}
for a list of FREE workshops, classes, mentoring, and health
coaching led by licensed clinicians and health educators in the
University Health Center.
\item Additional resources can be accessed through the UGA App.
\end{itemize}
\vspace{-2mm}
\section*{\normalsize Generative AI}
\vspace{-4mm}
Artificial intelligence (AI) tools, like chatGPT and other generative AI
chatbots, can be useful for improving text and computer code. However,
they can also hinder learning if used to generate answers and bypass
critical thinking. Students must disclose the use of generative AI for
completing assignments, including the final paper. If a
student decides to use generative AI, it can only be used to improve
text and code written by the student. AI tools cannot be used to create
answers by inputting assignment questions into prompts. Students
must report the prompts provided to AI tools, along with the original
text (or code) and the final text. Prompts and output can be disclosed
by copying and pasting screenshots into assignment documents.
\section*{\normalsize Tentative Course Outline}
\vspace{-6mm}
\begin{center}
\begin{tabular}[c]{lll}
\hline \hline
{\bf Date} & {\bf Lecture} & {\bf Reading} \\
\hline
\multicolumn{3}{c}{PART 1 -- BACKGROUND} \\
\hline
Aug 15 & Introduction & \\
\hline
%Aug 24 & Classical models of population dynamics & AHM1 Foreword, Preface, Chapter 1 \\
Aug 20 & Linear models & AHM1 Foreword, Preface, Chapter 1 \\
Aug 22 & Generalized linear models & AHM1 Chapter 3 \\
\hline
\multicolumn{3}{c}{PART 2 -- STATIC MODELS} \\
\hline
Aug 27 & Occupancy models & AHM1 Ch 4 and Ch 10 (pp 551--564) \\
Aug 29 & Occupancy models & \\
\hline
Sept 3 & Occupancy models & AHM1 Chapter 10 (pp 564--600) \\
Sept 5 & Occupancy models & AHM1 Chapter 10 (pp 591--600) \\
\hline
Sept 10 & Binomial $N$-mixture models & AHM1 Chapter 6 (pp 219--228) \\
Sept 12 & Prior predictive checks & AHM1 Chapter 6 (pp 229--245) \\
\hline
Sept 17 & Model selection & AHM1 Chapter 6 (pp 245--254) \\
Sept 19 & Goodness-of-fit & AHM1 Chapter 6 (pp 254--312) \\
\hline
Sept 24 & Multinomial $N$-mixture models & AHM1 Chapter 7 (pp 313--334) \\
Sept 26 & Multinomial $N$-mixture models & AHM1 Chapter 7 (pp 334--391) \\
\hline
Oct 1 & Hierarchical distance sampling & AHM1 Chapter 8 (pp 426--460) \\
Oct 3 & Conventional distance sampling & AHM1 Chapter 8 (pp 393--426) \\
\hline
Oct 8 & Non-spatial capture-recapture & SCR Chapters 1--4 \\
Oct 10 & Spatial capture-recapture & SCR Chapter 5 \\
\hline
Oct 15 & Spatial capture-recapture & SCR Chapter 7 \\
Oct 17 & Spatial capture-recapture & SCR Chapters 9 \\
\hline
\multicolumn{3}{c}{PART 3 -- DYNAMIC MODELS} \\
\hline
Oct 22 & Dynamic occupancy models & AHM2 Ch4 (Due: first draft) \\
Oct 24 & Dynamic $N$-mixture models & AHM2 Chapter 2 \\
\hline
Oct 29 & Survival models & AHM2 Chapter 3 \\
Oct 31 & Cormack-Jolly-Seber models & SCR Chapter 16 \\
\hline
Nov 5 & Jolly-Seber models & SCR Chapter 16 (Due: peer review) \\
Nov 7 & Jolly-Seber models & SCR Chapter 16 \\
\hline
Nov 12 & Dynamic spatial capture-recapture models & SCR Chapter 16 \\
Nov 14 & Dynamic spatial capture-recapture models & SCR Chapter 16 \\
\hline
Nov 19 & Dynamic spatial capture-recapture models & SCR Ch 16 \\
Nov 21 & Student presentation & \\
\hline
% \multicolumn{3}{c}{PART 4 -- STUDENT PRESENTATIONS} \\
% \hline
Nov 26 & Student presentations & \\
Nov 28 & Thanksgiving Break & \\
\hline
Dec 3 & No class (Friday schedule) & Due: Final paper \\
% \hline
% Dec 17 & Final exam (12:00-3:00) & \\
\hline \hline
\end{tabular}
\end{center}
The course syllabus is a general plan for the course; deviations announced to the class by the instructor may be necessary.
\end{document}