UNM Stat 427/527: Advanced Data Analysis I (ADA1)
Fall 2020 Syllabus is below tables Fall 2020
 Time: None/Always (Remote Arranged)
 Location: Zoom
 Stat 427.001, CRN 59508; Stat 527.001, CRN 59509
Step 0
Before our first “class” (Fri 8/21) please read through the following actions and install the required software on your computer. Install R (windows or mac) or upgrade, then RStudio.
 Install R video (5 min).
 Install R packages, also update all packages within RStudio.
 Set up your computer
 RStudio disable notebook
 Operating system to be more friendly to programming.
Goal
Learn to produce beautiful (markdown) and reproducible (knitr) reports with informative plots (ggplot2) and tables (kable) by writing code (R, tidyverse, Rstudio) to answer questions using fundamental statistical methods (all one and twovariable methods), which you’ll be proud to present (poster).
Course content
Weekly structure
(also see “Assessment” below) Preparation (Tuesday): Reading, Video, Quiz due Tue 11:59 PM.
 Worksheet 1 (Tuesday): Assignment due by Fri 11:59 PM.
 Worksheet 2 (Thursday): Assignment due by Mon 11:59 PM.
 UNM Learn for taking quizzes (graded automatically) and submitting assignments (evaluated by TA within 1 week).
 Lectures: YouTube Video playlist (try 1.5 speed, then pause as needed).
 Assignments: YouTube Video playlist
Course notes, code, data, and video lectures
Second text: PDS Textbook Notes from Fall 2019: ADA1_notes_F19.pdf includes all chapters in one document. Citing lecture notes example: Erhardt EB, Bedrick EJ, and Schrader RM. (2019) Lecture notes for Advanced Data Analysis 1. Retrieved Sep 1, 2019, from statacumen.com/teach/ADA1/notes/ADA1_notes.pdf, 136–144. Lecture notes for Advanced Data Analysis 1 (ADA1) Stat 427/527 University of New Mexico is licensed under a Creative Commons AttributionNonCommercialShareAlike 3.0 Unported License. Based on a work at https://statacumen.com/teach/ADA1/notes/ADA1_notes_F19.pdf.Ch  Chapter Title  Notes  R code  Datasets  Video lectures playlist  Helper videos 

00  Introduction to R, Rstudio, and ggplot  R  001 002  markdown, 01 PDS codebook, 01 HW codebook, 02 HW Lit review  
01  Summarizing and Displaying Data  R  011  03 HW 03 subset  
02  Estimation in OneSample Problems  R  021 022 023  
03  TwoSample Inferences  R  031 032 033  
04  Checking Assumptions  R  041  
05  OneWay Analysis of Variance  R  CHDS dat desc  051 (no videos recorded)  
06  Nonparametric Methods  R  061 onesample, 062 paired, 063 twosample, 064 ANOVA, 065 perm test.  
07  Categorical Data Analysis  R  071 intro, 072 single prop, 073 GOFtest, 074 two prop & cond prob, …  
08  Correlation and Regression  R  BodyMass dat desc pdf  081 corr/log, 082 corr hyp test, 083 LS reg eq, 084 085  
09  Introduction to the Bootstrap  R  091  
10  Power and Sample size  R  101  
11  Data Cleaning  R  111  14 HW to poster  
12  ADA2 Ch 11 Logistic Regression  R  121 122 123 124  Upgrading R on Windows 
PassionDriven Statistics (PDS) data
 NESARC Sampling Design, Codebook, RData. Alcohol abuse and related conditions.
 Unique ID “IDNUM”.
 AGE is in the data but not in the codebook.
 UNM Learn for taking quizzes (graded automatically) and submitting assignments (evaluated by TA within 1 week). Lectures: YouTube Video playlist (try 1.5 speed, then pause as needed).
 Assignments: YouTube Video playlist
 Erik’s example homework document: NESARC data, nicotine and depression.
 Use these files as a model for your assignments: .Rmd + .bib = .html.
 These are the files that Erik develops in the assignment videos: Rmd html
Timetable
Date  Class  Topic  Reading, Video, Quiz  class Worksheet, Data 

08/17  00  Install software, survey  Step 0 (above)  
08/18  01  
08/20  02 


08/25  03  Codebook 


08/27  04  
09/01  05  R programming, data subset and numerical summaries  
09/03  06  Plotting univariate  (Due date one day later for Labor Day)  
09/08  07  Plotting bivariate, numeric response  
09/10  08  Plotting bivariate, categorical response  
09/15  09  Simple linear regression, intro 


09/17  10 


09/22  11  Logarithm transformation 


09/24  12 


09/29  13  Correlation 


10/01  14  Categorical contingency tables 


10/06  15  Quiz 15, (NONE)  
10/08  Fall Break 1/2 (Wed 10/7)  Spurious Correlations  BBC Radio 4: More or Less, “sampling”, 9 min audio  
10/13  16  Parameter estimation (onesample) 


10/15  17  
10/20  18  Hypothesis testing (twosample) 


10/22  19  Paired data, assumption assessment  
10/27  20  ANOVA, posthoc comparisons 


10/29  21  
11/03  Fall Break 2/2 (Tue 11/03)  
11/05  22  Quiz 22, (NONE) 


11/10  23  Nonparametric methods 


11/12  24  Binomial and multinomial proportion tests  
11/17  25  Twoway categorical tables 


11/19  26  Simple linear regression, inference  
11/24  27  Quiz 27, (NONE)  
11/26  Thanksgiving break  Summary of Methods we’ve covered  
12/01  28  Logistic regression, intro  
12/03  29 


12/06  Finals week  (no final)  Congratulations on a great semester! 
Syllabus
 Description: Statistical tools for scientific research, including parametric and nonparametric methods for ANOVA and group comparisons, simple linear and multiple linear regression, and basic ideas of experimental design and analysis. Emphasis placed on the use of statistical packages such as R. Course cannot be counted in the hours needed for graduate degrees in Mathematics and Statistics.
 Prerequisite: Math 1350 [Stat 145] (or other intro stats course)
 Semesters offered: Fall
 Lecture: Stat 427.001, CRN 59508; Stat 527.001, CRN 59509; TR 15301645; Location: Zoom
 Email: Please include “ADA1” in the subject line of all emails.
Instructors
 Professor
 Erik Erhardt <erike@stat.unm.edu>, he/him
 Teaching Assistants
 Ola Anifowoshe <oanifowoshe@unm.edu>, he/him
 Jonathan Emery <jemery2016@unm.edu>, he/him
 Peer Learning Facilitators (PLF)
 John Romero <johnromero14@unm.edu>, he/him
 Pratap Khattri <pkhattri@unm.edu>, he/him
 Coby Segay <csegay@unm.edu>, he/him
 Jacob Matthew Moya <jmoya67@unm.edu>, he/him
Office hours
See email “ADA1, Stat 427/527, Announcements” from 8/23/20 for Zoom links and instructions.Time  Mon  Tue  Wed  Thu  Fri  Sat  Sun 
8 AM  
9 AM  
10 AM  JM  
11 AM  OA  OA  OA  CS  
12 PM  OA  OA  OA  PK  
1 PM  EE  EE  EE  
2 PM  EE  EE  EE  JM  JM  
3 PM  JE  JR  JE  JR  JM  JM  
4 PM  JE  JR  JE  JR  
5 PM  CS  JE  JR  JE  
6 PM  CS  PK  PK  
7 PM  PK  CS  PK  
8 PM  CS  
9 PM 
 We are also all available by appointment by email if these many hours do not work for you.
Student learning outcomes
At the end of the course, you will be able to: (student results: R, all years, 2015, 2014, 2013, 2012) General outcomes: Organize knowledge in graphs, tables, and code to support concise, comprehensible, and scientifically defensible written interpretations to produce knowledge within a reproducible research environment.
 Distinguish a testable scientific hypothesis or datasupported interpretation from an opinion.
 Understand from a data story the goals of the study and apply the correct statistical procedure.
 Explain the scientific aspects of a problem to nonscientists in a fashion that enhances understanding and decision making.
 Define parameters of interest and hypotheses in words and notation.
 Summarize data visually, numerically, and descriptively and interpret the observed characteristics. Calculate and interpret numerical summaries such as mean, variance, fivenumber summary, confidence intervals, and pvalues, and create visual summaries such as bar plots, scatter plots, and histograms. (Never pie charts!)
 Distinguish between statistical significance and scientific relevance.
 Use statistical software, such as R, to read and manage data, create informative plots, report numerical summaries, and apply statistical models, by recommended programming practice including abstraction and documentation.
 Understand the differences and limitations of controlled experiments and observational studies. Design experiments to infer causal treatment effects. Analyze observational data to infer associations between measured variables.
 Identify and explain the statistical methods, assumptions, and limitations used in reported studies in scientific literature or popular media.
 Evaluate and criticize published studies, the work of peers, and your own work and assess what was done well, what could be done better, and examine whether their conclusions are supported using statistical principles.
 Make evidencebased decisions by constructing and deciding between testable hypotheses using appropriate data and methods.
 Discover relationships and make predictions through model development and selection.
Meeting the learning outcomes
You will acquire new information in this class, but the emphasis is comprehending, integrating, and applying information. Rote factual memorization is the lowest form of learning. Effective learning takes place by explaining, integrating, applying, and analyzing facts, hypotheses, and theories. Learning in this class occurs by: Doing – completion of exercises that require analysis of data to answer questions and test hypotheses, or researching answers to reading assignments.
 Discussion – interaction with classmates to assemble and synthesize information utilizing the collective skills and knowledge base of the group.
 Listening, acting, and reflecting – activities during class time provide insights into information not available in readings and includes review difficult material to aid comprehension. Notetaking permits later reflection on lecture content. Listening to the professor lecture is the least effective learning tool for both students, however, and you should plan on coming to every class prepared to participate in active and reflective learning opportunities.
Assessment
 Quizzes will be due each Tuesday before class. Purpose: to assess reading and video comprehension and assure you’re prepared to actively participate in class activities with minimal lecture. (About 12, 20% of final grade.) Most weeks plan for 12 hours reading and video, 20minute quiz. Quizzes are not timed, they can be taken twice, and the higher of the two scores is used for grade calculation.
 Viewing quiz solutions after the due date in UNM Learn is not intuitive. Click on the “Begin” button (this is the nonintuitive part since you are not actually beginning the quiz), then click “View All Attempts” to see the scores. Finally, click the score in the “Calculated Grade” column to see the feedback for each question of the quiz.
 Worksheet assignments. Purpose: to struggle and find success in class with the concepts and skills. (About 24, includes class participation, 78% of final grade) Most weeks plan to finish in class.
 Course surveys are due at the end of the course (EvalKit). (About 1, 2% of final grade.)
 The lowest 2weeks worth of assignments are dropped, so your lowest 2 quizzes and 4 worksheet assignments are not included in the calculation of your grade.
Collaboration and citation
For homework, I encourage you to work together. Please discuss the data, code, and problems with one another, but do your own exploration and write up. We expect everyone to submit substantially different homework, and we will enforce this under the honor code. The small benefit you might get from plagiarism is not worth the severe penalty (of lost trust, being reported to the dean, no points for the assignment, etc.). As in life, please use any resources available to you. Projects and some homework will explicitly encourage you to use resources on the internet, but showing extra initiative will always be appreciated. You may find R programming tough at first, so feel free to discuss your problems with other classmates or meet with or email questions to me or the TAs. I encourage you to use the ideas of others, but make them your own, giving credit. For projects have a formal bibliography, for homework cite casually, and for code simply copy the URL in as a comment (which is doubly helpful for finding the resource again). You won’t be the first person to do anything in this class, so give credit where it’s due.Statements
Accommodations
In accordance with University Policy 2310 and the Americans with Disabilities Act (ADA), academic accommodations may be made for any student who notifies the instructor of the need for an accommodation. It is imperative that you take the initiative to bring such needs to the instructor’s attention, as I am not legally permitted to inquire. Students who may require assistance in emergency evacuations should contact the instructor as to the most appropriate procedures to follow. Contact Accessibility Resource Center at 2773506 for additional information. UNM is committed to providing courses that are inclusive and accessible for all participants. As your instructor, it is my objective to facilitate an accessible classroom setting, in which students have full access and opportunity. If you are experiencing physical or academic barriers, or concerns related to mental health, physical health and/or COVID19, please consult with me after class, via email/phone or during office hours. You are also encouraged to contact the Accessibility Resource Center at arcsrvs@unm.edu or by phone 2773506.Credithours
This is a threecredithour course. Class meets for two 75minute sessions of direct instruction for fifteen weeks during the semester. Students are expected to complete a minimum of six hours of outofclass work (or homework, study, assignment completion, and class preparation) each week.Title IX statement
In an effort to meet obligations under Title IX, UNM faculty, Teaching Assistants, and Graduate Assistants are considered “responsible employees” by the Department of Education (see page 15 of https://www2.ed.gov/about/offices/list/ocr/docs/qa201404titleix.pdf) requires that any report of gender discrimination that includes sexual harassment, sexual misconduct and sexual violence made to a faculty member, TA, or GA must be reported to the Title IX Coordinator at the Office of Equal Opportunity (https://oeo.unm.edu). For more information on the campus policy regarding sexual misconduct, see: https://policy.unm.edu/universitypolicies/2000/2740.htmlCitizenship and/or Immigration Status
All students are welcome in this class regardless of citizenship, residency, or immigration status. Your professor will respect your privacy if you choose to disclose your status. As for all students in the class, family emergencyrelated absences are normally excused with reasonable notice to the professor, as noted in the attendance guidelines above. UNM as an institution has made a core commitment to the success of all our students, including members of our undocumented community. The Administration’s welcome is found on our website: http://undocumented.unm.edu/.Support in Receiving Help and in Doing What is Right
I encourage students to be familiar with services and policies that can help them navigate UNM successfully. Many services exist to help you succeed academically and to find your place at UNM, see students.unm.edu or ask me for information about the right resource center or person to contact. UNM has important policies to preserve and protect the academic community, especially policies on student grievances (Faculty Handbook D175 and D176), academic dishonesty (FH D100), and respectful campus (FH CO9). These are in the Student Pathfinder (https://pathfinder.unm.edu) and the Faculty Handbook (https://handbook.unm.edu) Please ask for help in understanding and avoiding plagiarism or academic dishonesty, which can both have very serious disciplinary consequences.Land Acknowledgement
Founded in 1889, the University of New Mexico sits on the traditional homelands of the Pueblo of Sandia. The original peoples of New Mexico Pueblo, Navajo, and Apache since time immemorial, have deep connections to the land and have made significant contributions to the broader community statewide. We honor the land itself and those who remain stewards of this land throughout the generations and also acknowledge our committed relationship to Indigenous peoples. We gratefully recognize our history.Our Classroom
We’re doing this because: We want you to be empowered with statistics.
 We believe everyone should get out of this course with awesome skills
 Realtime feedback promotes efficient learning
GAISE Connections
Our six recommendations include the following: Teach statistical thinking.
 Teach statistics as an investigative process of problemsolving and decision making.
 Give students experience with multivariable thinking.
 Focus on conceptual understanding.
 Integrate real data with a context and purpose.
 Foster active learning.
 Use technology to explore concepts and analyze data.
 Use assessments to improve and evaluate student learning.
Learning without thought is labor lost. What I hear, I forget. What I see, I remember. What I do, I understand. – Confucius
Archive
Precourse todos
Did you receive a registration error for Fall 2020? Send me an email with the following answers: What registration error did you get (copy/paste is best)?
 What is your UNM ID?
 What is your Math/Stat background (that is, do you have the prerequisites)?
Course introduction materials
Problems installing PDS package? Solution. If you had problems installing the PDS package, no problem; here’s how to get the data: 1. Download the “.RData” file above for your dataset. 2. Where I have “library(PDS)” in my code, change it to the two lines below. You’ll need to update the “PATH_TO_FILE” below to the path on your computer’s hard drive, and “filename” needs to be changed to the name of the file. This will directly read the data file.
# library(PDS) setwd("/PATH_TO_FILE") load("filename.RData")
Unicode compile problems: If you knit to pdf you may get this error: “! Package inputenc Error: Unicode char”. ASCII is a small character set what we use to program in, Unicode is an extended character set that looks pretty (for example “straight quotes” become “curly quotes”) but causes code to break. You get unwanted Unicode when you copy/paste from a pdf or some other source into your code. To fix this, you have to find the Unicode and replace it with it’s ASCII equivalent. To do this: CtrlF to find, search for “[^\x00\x7F]” (without quotes), select “Regex” for regular expressions, and find the “Next” one. As it finds instances, replace the characters manually until there are no more. These characters will typically be curly quotes or fancy dashes.