UNM Stat 427/527: Advanced Data Analysis I (ADA1)
Fall 2019 Syllabus is below tables
Please complete Step 0 below.
Learn to produce beautiful (markdown) and reproducible (knitr) reports with informative plots (ggplot2) and tables (kable) by writing code (R, Rstudio) to answer questions using fundamental statistical methods (all one- and two-variable methods), which you’ll be proud to present (poster).
Course introduction materials
Did you receive a registration error for Fall 2019? Send me an email with the following answers:
1. What registration error did you get (copy/paste is best)?
2. What is your UNM ID?
3. What is your Math/Stat background (that is, do you have the pre-requisites)?
If you are waitlisted, as long as there are seats available I will override you into the course. Don’t worry.
Before our first class (Tue 8/20) please read through the following actions and install the required software on your computer and complete the brief survey. If you don’t have a computer, there are classroom computers which will be available only when the classroom is open. Video for this process.
- Complete surveys
- a short Opinio pre-survey required for classroom assessment (8/7 – 9/6/2019).
- Respondus survey about passion driven statistics (PDS) course content, by email (8/20 – 8/27/2019).
- Install R (windows or mac) or upgrade , then Rstudio. Videos that may be helpful:
- Install R packages, also update all packages within RStudio.
- Set up your computer
- (Postpone until later: Install LaTeX (for poster at end of the semester).)
(also see “Assessment” below)
- Pre-class (Tuesday): Reading, Video, Quiz due before class Tue 3:30 PM — solutions become available after the quiz is due.
- In-class (Tuesday and Thursday): Activities in class due by 5 PM the following day, submitted to UNM Learn (evaluated by TA within 1 week).
- Post-class (Thursday): Homework due the following Thursday by 3:30 PM, submitted to UNM Learn (evaluated by TA within 1 week).
Course notes, code, data, and video lectures
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 Attribution-NonCommercial-ShareAlike 3.0 Unported License. Based on a work at http://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||00-1 00-2||markdown,
01 PDS codebook,
01 HW codebook,
02 HW Lit review
|01||Summarizing and Displaying Data||R||01-1||03 HW 03 subset|
|02||Estimation in One-Sample Problems||R||02-1 02-2 02-3|
|03||Two-Sample Inferences||R||03-1 03-2 03-3|
|05||One-Way Analysis of Variance||R||CHDS dat desc||05-1|
|06||Nonparametric Methods||R||06-1 one-sample, 06-2 paired, 06-3 two-sample, 06-4 ANOVA, 06-5 perm test.|
|07||Categorical Data Analysis||R||07-1 intro, 07-2 single prop, 07-3 GOF-test, 07-4 two prop & cond prob, …|
|08||Correlation and Regression||R||BodyMass dat desc pdf||08-1 corr/log, 08-2 corr hyp test, 08-3 LS reg eq, 08-4 08-5|
|09||Introduction to the Bootstrap||R||09-1|
|10||Power and Sample size||R||10-1|
|11||Data Cleaning||R||11-1||14 HW to poster|
|12||ADA2 Ch 11 Logistic Regression||R||12-1 12-2 12-3 12-4||Upgrading R on Windows|
lm_diag_plots.R function for a large set of standard diagnostic plots.
Passion-Driven Statistics (PDS) data
I encourage you to use one of the AddHealth datasets. Use W1 if you want to understand adolescents when they were young and W4 if you want to understand adult relationships. NESARC is also interesting, but we had too many people choose many related questions in F15 from this dataset.
AddHealthW1 Sampling Design, Codebook, RData. Adolescents when they were young, unique ID “AID”.
AddHealthW4 Sampling Design, Codebook, RData. Same adolescents when they were older, unique ID “aid”.
NESARC Sampling Design, Codebook, RData. Alcohol abuse and related conditions, unique ID “IDNUM”.
OutlookOnLife Sampling Design, Codebook, RData. Interesting data, but not enough continuous variables to use, unique ID “CASEID”.
GapMinder Sampling Design, Codebook, RData. Country data, but it’s complicated to average large and small countries, unique ID “country”.
SEV LTER data
|Wk-Date||Cl||Topic||Reading, Video, Quiz||In-class Worksheet, Data||Homework|
|00-08/20||00||Install software, survey||Step 0 (above)||pre-survey required for classroom assessment (8/7 – 9/6/2019)|
|01-08/20||01||Intro, data, poster||read:
PDS Chs 2-3; video:
01 Syllabus subset,
01a Medical records Rmd html
Turn in assignment in Thursday’s class to learn how UNM Learn works.
|(Intro to using RMarkdown: Rmd html)|
01 Personal codebook
|In-class: yesterday’s 01a submit by 16:00
Work as a group, each submit own copy.
|HW: 01 Personal codebook Rmd html
Choose from PDS datasets
PDS Ch 2-4; video:
Lit Rev biblio & Mendeley; quiz:
02 codebook and lit review
|In-class: Rmd html
Turn in one question of variable association.
|(UNM Google Scholar)|
|02-08/29||04||Literature review||In-class: Rmd html
Turn in one citation to a research question.
|HW: 02 Literature review Rmd html bib|
|03-09/03||05||R programming, data subset and numerical summaries||read:
PDS Chs 5, 8, & 18,
Ch 00 R,
Ch 01 R; video:
Ch 00 p1,
Ch 00 p2,
Ch 01; quiz:
03 programming, univariate
|In-class: Rmd html
Look at datasets in R, create subset of data, rename variables, numerical summaries.
HW 03 vid
|In-class: Rmd html
Univariate plots of numerical and categorical variables.
|HW: 03 Data subset, univariate summaries and plots Rmd html
(See the link above the table “Erik’s NESARC data, nicotine and depression”.)
PDS Ch 9,
Ch 00 R,
Ch 11 R; video: 11-1; quiz:
|In-class: Rmd html
Complete at least one bivariate coding relationship.
|04-09/12||08||Data cleaning||In-class: Rmd html
Edit rules, run with dataset, assess exceptions, decide what to do with them.
|HW: 04 Rmd html|
|05-09/17||09||Simple linear regression, intro||read:
Ch 8.4, 8.2 R; video: 08-1 corr/log, 08-3 LS reg eq; quiz:
|In-class: Rmd html dat
Build intuition using SLR App, interpret properties of linear regression fit.
|05-09/19||10||Logarithm transformation||(novel example)||In-class: Rmd html dat
Plot, transform, plot, and interpret.
|HW: 05 Rmd html|
Ch 8.1, 8.3.1 R,
Ch 7.5.1 only sections on “conditional probability” and the following example R; video: 08-1 corr/log, 08-2 corr hyp test, 07-4 two prop & cond prob; quiz:
|In-class: Rmd html
Data collection (hand span and word memory), correlation, regression to the mean.
|06-09/26||12||Categorical contingency tables||quiz 06b, Guess Ages (for next in-class)||In-class: Rmd html d1
Interpret condition proportions in two examples.
|HW: 06 Rmd html|
Ch 2.1-2.2 R; video: see table above; quiz:
|In-class: Rmd html
Guess Ages, Legos.
(Legos part 2 Rmd html dat, diagram).
|BBC Radio 4: More or Less, “sampling” 9 min audio|
|07-10/03||14||Parameter estimation (one-sample)||In-class: Rmd html
Water on Earth.
|HW: 07 Rmd html
PDS Data Sampling Designs:
AddHealth, OOL, NESARC
|08-10/08||15||Hypothesis testing (two-sample)||read: Ch 2.3-end R
Ch 3 R; video: see table above; quiz:
|In-class: Rmd html
one- and two-sample tests using data we collected in class.
|08-10/10||Fall Break||HW: 08 Rmd html|
|09-10/15||16||Paired data, assumption assessment||read:
Ch 3.4 & 3.6,
Ch 5; video: see table above; quiz:
|In-class: Rmd html
Paired data and checking model assumptions.
|09-10/17||17||ANOVA, post-hoc comparisons||In-class: Rmd html
ANOVA, model assumptions, and paired comparisons.
|HW: 09 Rmd html|
Ch 10; video: see table above; quiz:
|In-class: Rmd html
NP one-sample tests and CIs, and ANOVA with pairwise comparisons.
|10-10/24||19||Binomial and multinomial proportion tests||In-class: Rmd html dat
Multinomial: World series number of games.
|HW: 10 Rmd html|
|11-10/29||20||Two-way categorical tables||read:
Ch 8.5-8.7; video:; quiz:
|In-class: Rmd html dat
|11-10/31||21||Simple linear regression, inference||In-class: Rmd html
Regression of height vs hand span using data from our class.
|HW: 11 Rmd html|
|12-11/05||22||Logistic regression, intro||read:
ADA2 Ch 11.1-3,
PDS Ch 16; video:; quiz:
|In-class: Rmd html
AddHealth W4 Pregnancy.
|Summary of Methods we’ve covered|
|12-11/07||23||Experiments and observational studies||In-class: Rmd html
Describing a study reported in the media.
|HW: 12 Rmd html|
|13-11/12||24||Statistical communication||read: PDS Ch 18; video:; quiz:
|In-class: Rmd html
Key statistical principles, ethics.With additional time, clarify which research questions you’ll present in your poster with a peer mentor. (Null results are ok!)
|Statistics is about communication, including writing and presenting.|
|13-11/14||25||Poster Preparation||In-class: Rmd html
Work on designing poster content at the bottom of your HW document.
|HW: 13 Rmd html
Work on your poster content.
Try to complete your poster planning in your HW document.
|14-11/19||26||Posters wrapping up||poster template
pdf, Rnw, sty, bib, logo
|Prof Erhardt’s example poster
|14-11/21||Thanksgiving break||move: Txgvg 11/28 next week|
|15-11/26||27||Show poster||In-class: Course evaluations, submit receipt (capture screen image) as in-class assignment.
See email for more details.
|HW: 15 Rmd html
Due next Wednesday 12/7. Complete and submit your poster in LaTeX pdf format.
|15-11/28||28||Approve poster, final touches||ARI Graphix
$9 poster printing
Open Mon-Fri 7:30-5:30
Do not use their website!
Subject: ADA1 class poster
Text: indicate to print “in color on bond paper”.
Attach: Poster pdf with your name in the filename, such as “FirstLast_ADA1_poster.pdf”.
Try to send by Friday noon for the poster to be ready by Monday.
Arrange to pick up the poster.
Price is $0.75/sq ft for Fall 2016.
|Have a peer mentor approve your poster for printing and presentation. Congratulations!|
|16-12/03||29||POSTERS||Poster sessions in SMLC Atrium||Poster Schedule (be on time):
3:40-4:40 Group 1
4:45-5:45 Group 2
5:50-6:50 Group 3
Congratulations on a great semester!
|16-12/05||30||Class finishes early||Erik traveling, no class|
|17-12/08||Finals week||(no final)|
(I reserve the right to continue to modify the schedule and improve the materials throughout the semester.)
Description: Statistical tools for scientific research, including parametric and non-parametric 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 1530-1645; Location: CTLB 300 (building 55, northeast of Zimmerman) Video
Laptops running R: I encourage you to bring a laptop to class each day so you can work on the exercises in class. If you don’t have one, no problem, there are laptops in class and teamwork is encouraged — sit next to someone friendly and discuss your work.
Saving data: If you’re using classroom computers, use Flashdrives or UNM’s OneDrive (available in LoboMail) for saving files. The CTLB computers do not connect to your standard UNM drive space (as of 2016, this may not still be an issue).
Please include “ADA1” in the subject line of all emails.
Erik Erhardt <firstname.lastname@example.org>, he/him, SMLC 312
Kelli Kasper <email@example.com>, she/her, SMLC 306
Leah Puglisi <firstname.lastname@example.org>, she/her, SMLC 319
Ola Anifowoshe <email@example.com>, he/him, SMLC 208
Additional Assistants, Peer Mentors, SEP
Grace Mayer, she/her
Mon: 11:00-14:00 Kelli
Tue: 13:00-15:00 Erik
Wed: 11:00-13:00 Leah
Thu: 13:00-15:00 Erik
Fri: 11:00-12:00 Erik
Student learning 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 data-supported 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, five-number summary, confidence intervals, and p-values, 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 evidence-based 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 you’d 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. Note taking 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.
- 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, the lowest few are dropped.) Most weeks plan for 1-2 hours reading and video, 20 minute 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 non-intuitive part, since you are not actually beginning the quiz), then click “View All Attempts” to see the scores. Finally, click “Calculated Grade” to see the feedback for each question of the quiz.
- In-class assignments are due by 5pm the next day, submitted to UNM Learn. Purpose: to struggle and find success in class with the concepts and skills. (About 24, includes class participation, 30% of final grade, the lowest several are dropped.) Most weeks plan to finish in class.
- Homework (HW) assignments are assigned each Thursday and due the following Thursday, submitted to UNM Learn. Purpose: to apply concepts and skills to your class poster project. (About 12, 30% of final grade, the lowest few are dropped.) Most weeks plan on 1-4 hours per assignment.
- Poster will be developed through semester (most HW assignment contribute to poster), the last couple weeks we’ll complete them, and the last week we’ll have poster presentations. Purpose: to have an overarching set of questions to answer using methods learned in the course, with a deliverable you can be proud of! (1 poster and presentation, 12% poster, 2% presentation, and 2% evaluations of others of final grade.) In the last couple weeks, assembling this poster may take 5-10 hours, using a template provided to you.
- Course surveys are due at the beginning and end of the course. Purpose: to participate in national project-based learning projects and improve course. (About 2, 4% of final grade.)
Final grade may include a small buffer at the discretion of the instructor. For example, final grade could be the total points earned divided by the total possible points times 0.95 for graduate students and 0.90 for undergraduate students. That is [Final Grade] = [Points Earned]/[Points possible * 0.95], so that your grade is slightly higher than you earned.
All assignments in this class are electronic, submitted to UNM Learn.
Late assignments will not be accepted.
Rubrics guide assessment (and self-assessment) of homework, code, projects, exams, and presentations. Each assignment will have its own specific rubric.
Use of R and RMarkdown are required for the course. This will include all of the R code for the assignment with the part of the problem it addresses in a fixed-width font and syntax highlighting. You will weave your code with prose narrations of your work and solutions.
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 discuss your problems with other classmates or meet with or email questions to the 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.
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 he/she are 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 277-3506 for additional information.
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 pg 15). This designation requires that any report of gender discrimination which 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. For more information on the campus policy regarding sexual misconduct.
UNM Indigenous Peoples Land and Territory Acknowledgment
I would like to acknowledge the original peoples of this land. The Sandia Pueblo (other pueblo communities) and the Navajo nation have ties and stories on this land and within the broader community that are connected within New Mexico. I am grateful to be able to work here in relationship and strengthen community on this territory.
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
- Real-time feedback promotes efficient learning
“It encourages me to engage actively with the course material and to take responsibility for my learning.”
Our six recommendations include the following:
- Emphasize statistical literacy and develop statistical thinking
- Use real data
- Stress conceptual understanding, rather than mere knowledge of procedures
- Foster active learning in the classroom
- Use technology for developing conceptual understanding and analyzing 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.
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")
Joining AddHealth waves 1 and 2 together into a single dataset can be done if you want to use variables from when the participants were both adolescents and adults. See Erik’s example project for the code.
Saving data: If you’re using classroom computers, use Flashdrives or UNM’s OneDrive (available in LoboMail) for saving files. The CTLB computers do not connect to your standard UNM drive space. I recommend using a very systematic folder structure, such as ADA1/HW, ADA1/Class, ADA1/Reading, ADA1/Poster, etc. Do not just work on files in your downloads folder or your desktop; respect your data and code!
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: Ctrl-F 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.
R is currently available (2016) in these UNM Locations: DSH 141 and 143, Econ 1004, SMLC pods, and SUB IT-LoboLab Pod and IT-LoboLab Classroom.
R style matters. There is a lot of online help on R, such as at UCLA, try-r, and Google’s Intro to R video series. Usually, try searching for “R [mytopic]” and you’ll get lots of results. ggplot2 plotting cookbook.
R reference card by Jonathan Baron.
Translate between MATLAB and R.
Statistical consulting and collaboration slides
Raster vs vector graphics.
Statistics pre-req refresher from Khan Academy.
Coursera has a free 4-week course on computing for data analysis with R.
Muddy points in perspective.
Asking smart questions
“Smart Questions” guide (note “hackers build things, crackers break them”)
Email Question Rubric:
* Send one email per question.
— Use “Reply” to continue conversation on a question; send a new email for a new question.
* Include “ADA1” as the first word of the subject line in new emails (if replying, just use reply).
* Begin email with a short question summary.
* When possible, include commented code in email body
— Comments should indicate where the problem is, what the expected behavior is, and what steps are necessary to reproduce problem.
— Code should include a “Minimum representative test cast” (http://www.catb.org/esr/faqs/
* If attaching code, please include all the files necessary to run your code (data, etc.).
LaTeX wiki, lshort, Detexify LaTeX symbols (linux texlive package management)
R tutorials: TryR (gentle), Kelly Black
R style matters. There is a lot of online help on R, such as at UCLA. Usually try searching for “R [mytopic]” and you’ll get lots of results.
Knitr in Rstudio (knitr is modern version of Sweave intro, demo, guide)
xtable to produce LaTeX tabular environment from R data.frames
Cookbook for R for helpful examples, visualization tutorials, diagrams
Image formats: vector (pdf, eps) vs raster (jpeg, bmp, tiff, gif)
Why stats now?
Table of selected statistical methods
Here’s a table of methods with the applicable semester of ADA and Chapter.
|continuous normal||not applicable
|normal||2 categories||mean||2 independent
rank sum test
|categorical||proportions||Chi square test
Fisher’s Exact test
signed ranks test
(3 or more
|categorical||proportions||Chi square test||1-07|
|2 or more
(e.g., 2-way ANOVA)
3 or more
|normal||not applicable||means||Repeated measures
|2 or more||normal||continuous||multiple linear
|Analysis of Covariance,
General Linear Models
|2||2 or more||normal||categorical||MANOVA||2-15|
|2 or more||2 or more||normal||continuous||multivariate
|2 sets of
2 or more
|0||normal||not applicable||canonical correlation||not|
|2 or more||0||normal||not applicable||factor analysis||not|
|0 or more||mixed categorical