StatAcumen.com | Acumen in Statistics

Time 2020-12-27 04:02:27

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This whitepaper with code addresses model issues and critiques about the use of a one-parameter model instead of a multi-parameter model in per-contact infectivity studies.... more As a Core Curriculum Teaching Fellow, my project will develop a new course called Statistics for Research  focusing on innovation, undergraduate research, and writing across the curriculum as an alternative to the traditional Introduction to Statistics, Stat 145. Intro Stats is one of the largest courses on campus with 1000-1200 students per semester in over 20 sections. This Statistics for Research course will cover the traditional material, but in a modern evidence-based way by integrating real data in the context of case studies, fostering active learning, and using technology to explore concepts and analyze large real datasets and communicate the results. This is a computer- and a project-based course in the style of Dierker s Passion-Driven Statistics and modeled directly after the already-successful UNM Stat 427/527 Advanced Data Analysis 1 and 2 where I ve piloted these learning strategies for advanced undergraduates and graduate students for four semesters.  Unlike my previous six-section intervention study showing active learning increases success by a third of a letter grade for everyone, this will be a pilot course developed for one or two sections. This implementation is just one of the many evidence-based recommendations I made as a 2016-17 Teaching Fellow for improving statistics education at UNM, including offering multiple versions (Stat Literacy with a first-year learning community, Stats for Research, Advanced Math-Stats); train/mentor our TAs prior to their teaching a course; offer a new Undergraduate Stat Ed Practicum course for all undergrad stat majors to serve as peer learning facilitators in at least one intro stat course; use multidisciplinary project-based learning to improve the outcomes of statistical interest, attitude, and condence for under-represented minority students; and make other small changes such as moving the final from the first day of finals at 7:30 AM to a later time when students are shown to have greater success. A long-term goal is to hire a professor of practice in statistics for continued leadership and research in statistical education at UNM.... more I m going to host an R Package Development R-Hack-a-Pack one-day workshop on Friday 8/17 from 10-5.  This is like a hack-a-thon , but, instead of tackling a dataset analysis, the goal is to learn and use the skills to package R code.  The first hour or so will cover the basic ideas of packaging code using modern tools such as RStudio, devtools, and usethis.  The rest of the day is intended as a protected time where you can turn your code into a package. We ll cover the basics of creating a package, package testing, writing vignettes, and using github (and CRAN) for version control and making your package available. If you already have a set of functions that you load with script( my_functions.R ), then you re an afternoon away from making a great package. If you have a large script with repeated code, then you can start by turning the repeated code into functions, package those functions, and write a short vignette to perform the same analysis using your package. If you have an idea for a new package to develop, bring that idea with you and we can consider trying to develop it during the workshop. My project is to package all the code and data for my two-semester data analysis course while I m not helping others.Food and helper:If you would like to volunteer to be a helper during the day for logistical issues, please email me directly.  It would be nice to have lunch and an afternoon coffee break with a snack.... more Enumerate Rmd code chunksI wrote the RmdNameChunk package to automatically name the Rmd code chunks. This is important for my workflow because I don t click Knit in RStudio, instead I run rmarkdown::render(fn). This has the advantage of using the console environment instead of the RMarkdown environment, so all the objects are available for manipulation in the console. However, it is hard to debug when there are scores of unnamed chunks. Now, I can easily name all the code chunk and can quickly identify where issues are.Install from github: https://github.com/erikerhardt/RmdNameChunkExampleInstall from source by running this command:devtools::install_github("erikerhardt/RmdNameChunk")Read an Rmd file, update existing prefixed code chunks, and renumber.library(RmdNameChunk)rmd_name_chunks( fn_in = "test_in.Rmd", fn_out = "test_out.Rmd", prefix_chunk_name = "chunk-")Review the input and output files to see how the chunk header names have been updated.Below is an example of the two Rmd files in the vignette.test_in.Rmd was read in and test_out.Rmd was created. The chunk headers are shown below from each file.test_in.Rmd8 : ```{r setup, include=FALSE}22 : ```{r cars}28 : ```{r}32 : ```{ r }36 : ```{r, echo=FALSE}40 : ```{ r, eval=FALSE}44 : ```{r , eval=FALSE}48 : ```{r chunk-2, eval=FALSE}52 : ```{r chunk-XXX , eval=FALSE}56 : ```{r chunk-XXX2 , eval=FALSE}60 : ```{r chunk-XXX3 , eval=FALSE}64 : ```{r chunk-XXX4 , eval=FALSE}68 : ```{r chunk-XXX5 , eval=FALSE}72 : ```{r chunk-XXX6 , eval=FALSE}81 : ```{r pressure, echo=FALSE}These code chunk headers were changed to those below:test_out.Rmd8 : ```{r setup, include=FALSE}22 : ```{r cars}28 : ```{r chunk-01}32 : ```{r chunk-02}36 : ```{r chunk-03, echo=FALSE}40 : ```{r chunk-04, eval=FALSE}44 : ```{r chunk-05, eval=FALSE}48 : ```{r chunk-06, eval=FALSE}52 : ```{r chunk-07, eval=FALSE}56 : ```{r chunk-08, eval=FALSE}60 : ```{r chunk-09, eval=FALSE}64 : ```{r chunk-10, eval=FALSE}68 : ```{r chunk-11, eval=FALSE}72 : ```{r chunk-12, eval=FALSE}81 : ```{r pressure, echo=FALSE}... more The resources below are helping me become a more disciplined writer capable of writing more first-author statistics papers. Since this is not an academic paper, I’m being loose about citation style but am including links, titles, and authors. The point is to write, not to stress about reviewing.1 How to write a lotVisiting my friend Jennifer in San Diego, I came across a book on her shelf that has motivated me to write more: “How to Write a Lot: A Practical Guide to Productive Academic Writing” by Paul J. Silvia.The main ideas that I took away from the book were well summarized in a University of Oregon post – “Becoming a Productive Faculty Writer – A Summary of Best Practices” – which also has a variety of helpful resources.The primary takeaways for me are: Write Daily. Write on a schedule and don’t move your writing for other meetings. Use phrases like “recurring intractable obligation” and “previously encombered temporal placement” to decline invitations. Have a Goal. Project goals, daily goals. Prewriting activities count. Stop at a Good Place. It gives you a better place from which to begin the next day. Jot down critical ideas to get started from. Limit Distractions. Shut the door and tune out the outside world. Take Care of Yourself. Eat well, sleep well, exercise well, and work well.2 Writing scientific manuscriptsThere is lots of harmonious advice for writing academic papers and getting these manuscripts through review and into publication. Below are the points of advice that resonated with me.My main conclusions are from these two sources (also Gelman): “Algorithm for writing a scientific manuscript” by Timothy R. O’Connor “The Baldwin Formula for scientific writing: writing papers and reviews” by Ian T Baldwin.  VideoO’Connor s algorithm overview is the order of parts to write that I m using as a basis below.  Baldwin s order is slightly different and indicated in each citation.[caption id="" align="aligncenter" width="240"] Overview of the formulation of a scientific manuscript. (O’Connor)[/caption]1. Figures/Tables“Construction of first-draft figures and tables based on data is the critical first step toward preparation of an outline for the manuscript.” (O’Connor)“Paste the figures and tables on a wall in their approximate order of appearance. This will provide the skeleton from which to begin the construction of a more detailed outline and draft.” (O’Connor)“Write a first draft of figure legends. Make each legend’s opening sentence into a figure title to describe the variables compared.” (O’Connor)“The entire story of your paper should be comprehensible from this abstract and the figures and tables.” (2b. Baldwin)“Each figure should illustrate at least one important take-home message of your paper and ideally be understandable in 30 seconds to an uninformed scientific reader.” (Baldwin)Caption: “the first sentence should summarize the main point of the figure.” “The entire figures should be fully comprehensible from the figure caption.” “Table legends should include only a stand-alone first sentence.” (Baldwin)For more on figures, see our chapter in the 4th ed of the “Handbook of Psychophysiology”.2. Summary Statements“These important statements are conclusions summarizing the major contributions of the manuscript to the scientific community. Use short rigid statements usually containing cause/effect words.” (O’Connor)3. Scientific AudienceIdentify the scientific audience and journals. (O’Connor)4. Materials and Methods“Write the materials and methods section to supplement and explain the figure legends.” (O’Connor)“Write while you are still conducting experiments.” (1.+4. Baldwin)5. Re-evaluate Data“For each figure and table, make a note of which summary statement it addresses.” (O’Connor)6. Results“Once each figure and table has a legend describing the mathematical variables compared, then the first sentence of each results paragraph is simply the results of this comparison.” (O’Connor)“The Results section should highlight all of the conclusions that you can draw from your data.” (3. Baldwin)7. Discussion/Conclusions“Convert by logical arguments the relations of mathematical variables stated in the results section into mechanistic interpretations of cause and effect. Simply restate the data relation from each results paragraph and convert each to mechanistic conclusions.” (O’Connor)Table 1 (O’Connor) gives examples of results words for data relations vs. discussion words for logic and mechanism.“The discussion should start with a paragraph which succinctly states your motivation, and the conclusions that you draw from your data that do not require discussion and ends with an introduction to the weaker conclusions that you would like to draw, but do require discussion.” “The following paragraphs should discuss the conclusions that you would like to draw from your data, but require discussion because the inferences are indirect, or your data or the data in the literature are contradictory.” “The last paragraph should summarize all major conclusions from the discussion of your results and indicate future research directions.” (6. Baldwin)8. ReferencesThis is taken care of by a reference manager with well-curated reference data and style file.9. Introduction“First, summarize the subject and review the literature to allow the reader to (i) understand the statements in the Results and Discussion, (ii) understand how the statements fit into the extant scientific body of knowledge, and (iii) Understand that the conclusions are indeed novel, the next step in the knowledge of the subject.” (O’Connor)“Write the last paragraph of the Introduction first; this should be an abbreviated road map of the question that you are addressing and the means by which you answered the question” (5. Baldwin)“Circle all of the words and concepts that you used in this last paragraph that need to be introduced and elaborated on in preceding paragraphs of the Introduction. In this way, you will be reverse engineering the entire Introduction from your last paragraph.” (Baldwin)Remove the fluff.10. Title“The title should be a positive statement from the summary statements.” (O’Connor)11. Conclusion Paragraph“In this paragraph, restate the logical conclusions and explain why these conclusions are important, how they will influence future thinking in this and other fields. In the introduction, these conclusions were the next step. Now discuss the future based on the conclusions in this manuscript or an alternative path to further substantiate the validity of your conclusions. Also, state the relevance of results in the present manuscript to other fields.” (O’Connor)12. Abstract“Use the abstract in general terms to describe the most important points in the work.” (O’Connor)“Write a rough draft of the abstract … to create the roadmap of the logic of the results and conclusions that you will be developing.” (2b. Baldwin)13. Revise, revise, revise.Erase your memory of your writing and see it fresh. Ask others to read it. Read it after time has passed. Have someone read it to you. (Baldwin)When you can’t find the phrase to get you started, start with “70 useful sentences for academic writing” by Luiz Otávio Barros.4 PresentationsUse story structure in the first five slides to set up the scenario and characters in your heroic journey. Chapter 4 of Cliff Atkinson’s “Beyond Bullet Points” tells you how.Introduction: The Setting Headline (Where am I, and when is it?) The Role Headline (Who am I in this setting?) The Point A Headline (What challengee do I face in this setting?) The Point B Headline (Where do I want to be?) (The Gap Between A and B) (Why am I here?)Body:Chapter 5 was also helpful for structuring the remaining slides in a hierarchy of key points (sections) with explanations (subsections) and details (slides).Key Point 1Analysis 1Fact 1Fact 2Fact 3Analysis 2Fact 1Fact 2Fact 3Analysis 3Fact 1Fact 2Fact 3Key Point 2Analysis 1Fact 1Fact 2Fact 3Analysis 2Fact 1Fact 2Fact 3Analysis 3Fact 1Fact 2Fact 3Key Point 3Analysis 1Fact 1Fact 2Fact 3Analysis 2Fact 1Fact 2Fact 3Analysis 3Fact 1Fact 2Fact 3Conclusion (recap):The Point A Headline (What challengee do I face in this setting?)The Point B Headline (Where do I want to be?)(The Gap Between A and B) (Why am I here?)The Call to Action Headline (How do I get from A to B?)... more I m enjoying Sabbatical during the Fall 2017 Spring 2018 academic year.  My Sabbatical Leave Plan includes visiting both UC Irvine and the Mind Research Network to: learn more about Bayesian graphical models, learn more about Hamiltonian Monte Carlo (HMC), learn about their statistical and computational implementations, and apply both to extend current models in the application to fMRI brain imaging data. Continue UNM 100-level statistics and mathematics education initiatives to understand factors influencing studentsuccess and find strategies to increase success.... more Richard Wilson book page includes purchasing details.Six and a half years ago we called for contributions.  Now we contribute this book back to the FolkMADS community.Introduction to the first editionThis book is the fruit of an old idea, a long fallow period, and a final burst of enthusiastic commitment. The idea was to provide Richard with a meaningful focus and contribution during his last year of life. He wrote and wrote, filling notebooks; Lauren transcribed what she could. We photocopied all his cards that could be found in October 2010; Katherine provided an initial transcription. This book has taken many forms in its many revisions and reimaginings: experimenting with different paper sizes, interleaving the stories from other people in with his own story, modifying the dance formats, and finally returning to this fairly simple format. The long lull, after much compilation and redrafting, was partly due to my grieving after Richard passed; with Richard gone the urgency of the project had passed, since my primary commitment was to him. Then I allowed other projects to take over, including the trials of earning tenure as faculty at UNM. Finally, after almost six years, it is done.While I may not have been able to realize the book I envisioned, this is it. I m heartened by a thoughtful and generous community to whom I present this gift and tribute. Five years since Richard s passing, I still feel his spirit and gentleness as I teach new dancers and callers, just as he taught me, feeling how each foot lifted is as important as how each is set upon.Erik Barry ErhardtAlbuquerque, NMOctober 2016... more Albuquerque The Magazine gave me the opportunity to say what I love and don t about Albuquerque.Thumbs Up: FolkMADS. I love contributing to and connecting to the living traditions of community-centered American and Western European folk music and dance in New Mexico, from the English influences from the late 1600s, to the local Rocky Mountain squares from the 1820s, through to the current Modern Urban Contra dances we enjoy each week.Thumbs Down: Goatheads. I m optimistic for Albuquerque s Parks and Rec department s strategy to plant native grass along a portion of the city’s 170 miles of trails to squeeze out the goatheads and their spiny little seeds.  Here s another option:  host-specific, puncturevine eating weevils.[caption id="attachment_2715" align="aligncenter" width="408"] Albuquerque The Magazine, November 2015, p. 35[/caption]... more In Vivo Inhibition of miR-155 Promotes Recovery after Experimental Mouse StrokeErnesto Caballero-Garrido, Juan Carlos Pena-Philippides, Tamar Lordkipanidze, Denis Bragin, Yirong Yang, Erik Barry Erhardt, and Tamara Roitbak.The Journal of Neuroscience, 35(36), pdf, 12446-12464Online: September 9, 2015http://www.jneurosci.org/content/35/36/12446.short?sid=d532fe0d-f727-4729-8f7c-ab2cf8a1e7f7DOI: 10.1523/JNEUROSCI.1641-15.2015AbstractA multifunctional microRNA, miR-155, has been recently recognized as an important modulator of numerous biological processes. In our previous in vitro studies, miR-155 was identified as a potential regulator of the endothelial morphogenesis. The present study demonstrates that in vivo inhibition of miR-155 supports cerebral vasculature after experimental stroke. Intravenous injections of a specific miR-155 inhibitor were initiated at 48 h after mouse distal middle cerebral artery occlusion (dMCAO). Microvasculature in peri-infarct area, infarct size, and animal functional recovery were assessed at 1, 2, and 3 weeks after dMCAO. Using in vivo two-photon microscopy, we detected improved blood flow and microvascular integrity in the peri-infarct area of miR-155 inhibitor-injected mice. Electron microscopy revealed that, in contrast to the control group, these animals demonstrated well preserved capillary tight junctions (TJs). Western blot analysis data indicate that improved TJ integrity in the inhibitor-injected animals could be associated with stabilization of the TJ protein ZO-1 and mediated by the miR-155 target protein Rheb. MRI analysis showed significant (34%) reduction of infarct size in miR-155 inhibitor-injected animals at 21 d after dMCAO. Reduced brain injury was confirmed by electron microscopy demonstrating decreased neuronal damage in the peri-infarct area of stroke. Preservation of brain tissue was reflected in efficient functional recovery of inhibitor-injected animals. Based on our findings, we propose that in vivo miR-155 inhibition after ischemia supports brain microvasculature, reduces brain tissue damage, and improves the animal functional recovery.SIGNIFICANCE STATEMENTIn the present study, we investigated an effect of the in vivo inhibition of a microRNA, miR-155, on brain recovery after experimental cerebral ischemia. To our knowledge, this is the first report describing the efficiency of intravenous anti-miRNA injections in a mouse model of ischemic stroke. The role of miRNAs in poststroke revascularization has been unexplored and in vivo regulation of miRNAs during the subacute phase of stroke has not yet been proposed. Our investigation introduces a new and unexplored approach to cerebral regeneration: regulation of poststroke angiogenesis and recovery through direct modulation of specific miRNA activity. We expect that our findings will lead to the development of novel strategies for regulating neurorestorative processes in the postischemic brain.... more Erik Barry Erhardt, PhD, is an Associate Professor of Statistics at the University of New Mexico Department of Mathematics and Statistics, where he has served as Director of the Statistics Consulting Clinic, and is currently Director of the Biostatistics and NeuroInformatics (BNI) Core for the second phase of the Center for Biomedical Research Excellence (COBRE) in Brain Function and Mental Illness at the Mind Research Network. His research interests include Bayesian and Frequentist statistical methods for stable isotope sourcing and brain imaging. Erik is a Howard Hughes Medical Institute Interfaces Scholar collaborating in interdisciplinary research and offering consulting services in statistics. Links Curriculum Vita (w/extras)Curriculum Vita (UNM)Research StatementTeaching DossierService StatementGoogle ScholarcitationsORCIDresearcher IDSISUSsoftware for stable isotope sourcingBlogfor updates and reflection

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