Dr. Jonathan E. Nyquist https://sites.temple.edu/geophysics Department of Earth and Environmental Science, Temple University Tue, 19 Dec 2023 15:57:18 +0000 en-US hourly 1 https://wordpress.org/?v=6.4.3 Early Detection of At-risk Students – Then What? https://sites.temple.edu/geophysics/2023/12/19/early-detection-of-at-risk-students-then-what/ https://sites.temple.edu/geophysics/2023/12/19/early-detection-of-at-risk-students-then-what/#respond Tue, 19 Dec 2023 15:25:02 +0000 https://sites.temple.edu/geophysics/?p=1152 Continue reading ]]> According to the National Center for Education Statistics (NCES, 2022), only 64% of undergraduate students starting at a four-year institution in 2014 completed their degree within six years. Temple University, like all higher eduction institutions, is continually looking for ways to boost student retention, academic progress, and graduation rates.

Temple has a long-standing policy of issuing midterm progress ratings for all undergraduates. Students receive feedback from their instructors on whether their work is Satisfactory (S), or Unsatisfactory (U) for reasons of Attendance (A), poor Grades (G), Missing assignments (M), or insufficient Participation (P), or a combination of factors. Thus, a student receiving a U-AM has poor attendance and missing assignments. Colleges follow up with emails to struggling student to encourage them to seek assistance from instructors, advisors and the many support services available to Temple undergraduates.

A logistic regression analysis showed that midterm progress ratings are highly predictive of final grades. Students with receiving a U rating for one or more reasons were 14 times more likely to receive an unsatisfactory final grade or withdraw from the course. Are midterm progress ratings and subsequent messaging ineffective, or do the warnings simply come to late for struggling students to turn it around?

In a poster I will present at Temple University’s 22nd Annual Faculty Conference on Teaching Excellence (January 10 & 11, 2024), I will discuss a study conducted while I was Director of General Education at Temple to see: (1) whether Canvas LMS data could be used to identify at-risk students earlier in the semester, and if so, (2) whether issuing the same warning earlier would improve student outcomes. Spoiler alert: using Canvas data it proved possible to detect at-risk students as early as weeks 3-4, however, reaching out to these students earlier did not improve outcomes. The literature on the use of big data, machine learning algorithms, and AI to detect as-risk students is growing exponentially, while research on effective intervention lags sadly behind (Motz et al, 2023).

References

Motz, B., Bergner, Y., Brooks, C., Gladden, A., Gray, G., Lang, C., … & Quick, J. (2023). Lak of direction. Journal of Learning Analytics, 1-13. https://doi.org/10.18608/jla.2023.7913

National Center for Education Statistics. (2022). Undergraduate Retention and Graduation Rates. Condition of Education. U.S. Department of Education, Institute of Education Sciences. Retrieved [19 Dec. 2023], from https://nces.ed.gov/programs/coe/indicator/ctr.

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Hysteresis in Archie’s Law https://sites.temple.edu/geophysics/2023/08/30/hysteresis-in-archies-law/ https://sites.temple.edu/geophysics/2023/08/30/hysteresis-in-archies-law/#respond Wed, 30 Aug 2023 17:32:51 +0000 https://sites.temple.edu/geophysics/?p=1147 Continue reading ]]> My former student and newly minted Ph.D., Dr. Gina Pope, and I recently had a paper accepted in the Journal of Environmental and Engineering Geophysics. We think the paper is important because is shows the necessity of monitoring the pore fluid conductivity when using electrical resistivity to track water infiltration. Applying Archie’s Law assuming the pore fluid conductivity remains constant may yield erroneous saturation estimates. The same resistivity value can correspond to different moisture levels depending on whether the soil is wetting or drying out.

Apparent Hysteresis in Archie’s Law: Implications of Changing Pore Fluid Conductivity for Electrical Resistivity Monitoring of Infiltration

Gina Ginevra Pope and Jonathan E. Nyquist

Abstract

The electrical resistivity of the vadose zone is highly dependent on soil moisture content, making resistivity tomography a potential tool for non-intrusive monitoring of infiltration. There is a long history of using petrophysical relationships such as Archie’s law to convert resistivity values to volumetric water content, often under the assumption that the pore fluid conductivity is constant. Analysis of two years of nearly continuous soil conductivity and moisture data from sensors buried in a bioswale in Philadelphia, Pennsylvania showed that the characteristic curve of volumetric water versus soil resistivity exhibited hysteresis. The same value of electrical resistivity was associated with different degrees of saturation during imbibition and drying. Accurate water content could be estimated using Archie’s law only when changes in pore fluid conductivity were incorporated.  In addition to the cyclic changes with each rain event, pore fluid conductivity varied throughout the year, with the highest values recorded during the winter due to road salt runoff, followed by a gradual decline with each rain event. Cementation and saturation exponents differed for sensors within 25 cm of each other despite the uniform nature of the bioswale fill material and despite fits to Archie’s Law for individual sensors, indicating considerable heterogeneity. A pattern of changing pore fluid conductivity in response to storms was confirmed at two additional sites with soil moisture and bulk conductivity sensors. Assuming that the conductivity of the pore fluid remains constant during infiltration not only produces erroneous soil moisture estimates, it can even reverse the apparent soil moisture trend. We conclude that to use electrical resistivity to monitor infiltration it is essential to independently record changes in pore fluid conductivity, and that multiple sensors are required because changes in pore fluid conductivity, as well as Archie parameters, can vary on a sub-meter scale for even apparently homogeneous sites. Additionally, long-term changes in Archie parameters, notably  are possible, and may indicate long-term changes in soil fabric.       

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Program Like a Martian – An Introduction to Python Programming https://sites.temple.edu/geophysics/2023/07/31/program-like-a-martian-an-introduction-to-python-programming/ https://sites.temple.edu/geophysics/2023/07/31/program-like-a-martian-an-introduction-to-python-programming/#respond Mon, 31 Jul 2023 14:34:03 +0000 https://sites.temple.edu/geophysics/?p=1141 Continue reading ]]> Back in 2016-2017, Temple’s General Education office created a new course named Demystifying Technology. The novel idea was to offer six modules taught by six different instructors in a single semester: Algorithmic and Computational Problem Solving (2 weeks); Internet, Culture and Society (2 weeks); Global Networks and Economies (2 weeks); Coding and Applied Computer Science (4 weeks); Entrepreneurship, Creativity and Design Thinking (2 weeks); and Big Data and the Information Explosion (2 weeks). Ultimately, the design was deemed unwieldy — the two week modules, in particular, were just too short — but it was an interesting experiment.

I developed and taught the four week Coding and Applied Computer Science model. Given that the audience was comprised of general education students, many of whom were freshman, most with zero prior programming experience, I wanted the nodule to be a gentle introduction to programming in python while simultaneously showcasing the power of the language. To make it fun, I built the exercises around the best-selling book movie, The Martian, which was made into a movie staring Matt Damon. The story is futuristic version of Robinson Crusoe: astronaut Mark Watney, stranded alone on Mars after an accident, struggles to survive until a rescue mission can arrive. I created a series of Jupyter notebooks where students write python programs to solve some of the challenges Watney faced.

I have successfully used this series of notebooks as a self-guided introduction to python programming for several graduate and undergraduate student researchers. While there is no shortage of python tutorials on the internet, some of you might still find this one fun and useful. I have recently revised the notebooks to be compatible with Google Colab, updated all the links, and posted the Jupyter notebooks and supporting data in a repository on GitHub. Never let old course preparation go to waste!

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Rain clouds and Old Faithful https://sites.temple.edu/geophysics/2023/06/23/rain-clouds-and-old-faithful/ https://sites.temple.edu/geophysics/2023/06/23/rain-clouds-and-old-faithful/#respond Fri, 23 Jun 2023 17:15:18 +0000 https://sites.temple.edu/geophysics/?p=1135 Continue reading ]]> On my TODO list for this summer summer is preparing to teach Elements of Data Science for the Physical and Life Sciences in the fall. One of the labs in the class uses data collected on eruptions of the famous Old Faithful geyser in Yellowstone National Park. The data come from a classic 1990 paper by Azzalini and Bowman that has 299 measurement pairs of the time between the start of geyser eruptions and the how long each eruption lasted. The relationship is an approximately linear — the longer the wait since the last eruption the greater the duration of the next eruption.

Notice that the distribution is bimodal, forming two obvious clusters. You can see this with a simple histogram plot of duration.

“Raincloud plots,” as highlighted in this recent blog post, are another way to show data distributions. Raincloud plots, also called “pirate plots” (by the R community, naturally, Arrh!) combine three different kinds of plots: (1) a Box plot, a jittered strip plot (the rain), and a density plot, a sort of a smoothed, normalized histogram (the raincloud). Below are raincloud plots of the duration and time between eruptions (the wait).

What I like is the way the three plot elements compensate for each other. The Box plot doesn’t capture the bimodal distribution but he density plot makes up for this, and the strip plot of the data points helps with the visualization. The three together provide a nice, intuitive feel for how the data are distributed.

Raincloud plots are relatively new. The debate is ongoing about the best way to construct them. Read the blog post to learn more or or the original paper for a more in-depth discussion. To learn more about the Old Faithful data and the geologic mechanisms behind the deyser eruption timings, I encourage you to read the Azzalini and Bowman’s paper.

Azzalini, A., & Bowman, A. W. (1990). A look at some data on the Old Faithful geyser. Journal of the Royal Statistical Society: Series C (Applied Statistics)39(3), 357-365.

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Evolving Soil Moisture Patterns at SMP I & J https://sites.temple.edu/geophysics/2023/05/25/evolving-soil-moisture-patterns-at-smp-i-j/ https://sites.temple.edu/geophysics/2023/05/25/evolving-soil-moisture-patterns-at-smp-i-j/#respond Thu, 25 May 2023 15:10:06 +0000 https://sites.temple.edu/geophysics/?p=1115 Continue reading ]]> Temple and Villanova installed a network of soil moisture sensors at a depth of 10 cm at the newly renovated Stormwater Management Projects I and J along the flank of Highway I-95. Tracking the near-surface soil moisture history is important for understanding plant health in the basins. The sensors also monitor electrical conductivity, which we plan to use to track road salt influx during the coming winters.

Below is an image of the soils sensor locations superimposed on a digital elevation model of the two basins created from LiDAR data collected at the site.

The image colors show the lower topography in browns shading to the higher topography in greens, but as you can see from the photograph, the entire relief is only a few meters. The sensor IDs start with I (Basin I) or J (Basin J) and are numbered followed by a letter: O for sensors near an outlet, I for sensors near and inlet, B for sensors along the floor of the basins, and R for reference sensors place on the basin flanks above anticipated flooding levels.

Preliminary results show that moisture levels between storm events are highly variable across the basins. So to visualize the changes in soil moisture with storms, I have plotted only the changes in volumetric water content (m3/m3) for each sensor relative to its starting value on Feb 22, 2023. In the figure below the top graph shows the VWC at sensor J8-I near the inlet in the upper left of the figure above, which lets us see precipitation events. The figure below that shows the soil moisture sensor locations color-coded to show changes in VWC using a divergent color palette — reds for drying, blues for wetting, superimposed on a grayscale version of the DEM shown above.

It is interesting to observe that for none of the three storms does the basin fill. A few of the sensors along the floor of the basin show moisture increases, but no prolonged saturation. This suggests that eight it takes a large storm to flood this basin, or the outlet threshold is too low and needs to be adjusted to allow water to pond for infiltration. We will know better after we have enough data to include larger summer storms.

CLICK on the image below to see the animation. The animation advances in four-hour increments.

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ERT Surveys to Guide Infiltration Measurements https://sites.temple.edu/geophysics/2023/04/26/ert-surveys-to-guide-infiltration-measurements/ https://sites.temple.edu/geophysics/2023/04/26/ert-surveys-to-guide-infiltration-measurements/#respond Wed, 26 Apr 2023 14:05:23 +0000 https://sites.temple.edu/geophysics/?p=1032 Continue reading ]]> For several years now, I have been part of a team of researches from Temple and Villanova universities that is assisting the Pennsylvania Department of Transportation (PennDOT) with the design and monitoring of bioswales, which are landscaped basins being constructed adjacent to I-95 to manage stormwater runoff as part of ongoing renovations to this key north-south highway. The goal of the bioswales is to promote stormwater infiltration, recharging the groundwater rather than routing all of the flow to overburdened sewage treatment plants. Just how much infiltration occurs depends on how easily water percolates into soil underlying the basins.

Infiltration measurements are made to characterize percolation, but given the heterogeneous nature of urban soil, which can contain anything from sand to clay to construction debris, deciding where to make infiltration measures is challenges. Last summer, I tested using electrical resistivity tomography (ERT) to guide these measurements.

The ERT cable ran down the central axis of the bioswale while it was still under construction. Infiltration measurements were later performed along the same line targeting heterogeneities detected by this survey.


Because clay soils have both a lower electrical resistivity and lower infiltration rate than sandy soils, the ideas was to used resistivity images to guide the location of infiltration measurements. As the resistivity cross-section below shows, there was excellent agreement. Where the resistivity was low, so was the measure infiltration.The idea of using resistivity measurements to assess infiltration potential is not new. Many examples can be found in the literature. Here is one recent example. But it was gratifying how well it worked in this instance!

Shows a resistivity cross-section down the axis of basin extending to a depth of over 5 m. The blue regions are low resistivity, hence more likely rich in silt/clay. The Villanova team measured significant resistivity only in the small pockets of higher-resistivity soil.
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Geopython 2023 in Basel, Switzerland https://sites.temple.edu/geophysics/2023/03/27/geopython-2023-in-basel-switzerland/ https://sites.temple.edu/geophysics/2023/03/27/geopython-2023-in-basel-switzerland/#respond Mon, 27 Mar 2023 15:53:59 +0000 https://sites.temple.edu/geophysics/?p=1004 Continue reading ]]> This month I attended the Geopython 2023 conference in Basel, Switzerland. This was a well-organized conference with between 100-200 in-person attendees. The focus of most of the talks was on geospatial applications, particularly the rise of machine learning algorithms is geospatial data processing.

Geopython 2023

For example, Mikolaj Czerkawski, PhD student at the University of Strathclyde in Glasgow, gave an interesting talk entitled, “Generating Clouds in Satellite Images with SatelliteCloudGenerator.” Why would you want to generate clouds to obscure your satellite images, particularly in Scotland where there are plenty of clouds already? You need lots of training examples to teach machine learning algorithms how to remove them. It turns out generating clouds isn’t easy because their impact on satellite imagery depends on the spectral band. Very interesting!

Simulating Clouds (https://github.com/cidcom/SatelliteCloudGenerator)

Another talk I found fascinating was “Automated weeding of railway tracks” presented by Sven Schmitz-Leuffen. Weeding railways may not sound interesting at first, but the system involves a specially designed train engine equipped with GPS sensors, trained AI plant detectors and a cartographic computer controller that ensures herbicide is not applied in areas spraying is not allowed, such as populated areas, over waterways, etc. All of this is done in real time as the train is cruising along the tracks — a very clever application of python and geospatial processing!

There were many more fascinating talks and workshops. You can find the full list here.

Of course, Switzerland is such a beautiful country, and the trains make it so easy to get around that I combined the conference with a vacation, including a trip to Zermatt to view the Alps, and to tour the Lindt Chocolate factory outside Zurich. Overall, a wonderful trip!

Viewing the Matterhorn
A nine meter high chocolate fountain at the Lindt factory outside Zurich.
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Zeros and the Power of Junk on Time https://sites.temple.edu/geophysics/2023/01/30/zeros-and-the-power-of-junk-on-time/ https://sites.temple.edu/geophysics/2023/01/30/zeros-and-the-power-of-junk-on-time/#respond Mon, 30 Jan 2023 17:08:18 +0000 https://sites.temple.edu/geophysics/?p=997 Continue reading ]]> Many years ago, when I worked at Oak Ridge National Laboratory, I remember complaining to a senior colleague that some of the massive project reports we received from consulting firms were little more than a brief introduction and a boiler-plate methods section duplicated from previous reports, very little in the way of conclusions, and pages upon pages of appendixes comprised of printed tables of raw data. My colleague informed me that these reports still satisfied contractual obligations. To be fair to the consultants, problems with permitting, weather or equipment troubles in the field, and delays in getting results back from the lab, often left the report writers facing a contractual deadline with no time for data analysis or reflection. Given the choice between providing “junk on time” or facing financial penalties for filing a late report, along with the potential loss of future contacts, they generated thick reports that provided few insights and no constructive recommendations. 

Decades later, now a professor, as I look at the records of struggling students, I’m struck by how often they fail, not because they received poor grades, but because they simply did not submit the assignments — they did not recognize the importance of submitting junk on time.

Yes, yes, it would be far better to read critically, to reflect thoroughly, and to start assignments early, leaving plenty of time for revision. I am by no means an advocate for skating by with substandard work. But when life happens, and you simply do not have the time to do it properly, all professionals know you either negotiate a new deadline (the best option), or you work with the time available. You do not blow off the assignment. In the working world, this will get you fired. As a student, zeros will destroy your chances of passing the course.

Let’s compare two hypothetical students; I’ll call them Joe and Moe. Joe is gifted academically, so when he does the work he scores well, but he often skips assignments. Moe, on the other hand, is not as gifted but never fails to turn in something. When pressed for time he turns in really poor work — junk that earns a crummy 50/100. The rest of the time we’ll assume he typically gets a B-.

Ten assignments:

Joe’s Scores:

95, 0, 91, 92, 0, 0, 100, 0, 90, 0

Moe’s Scores:

82, 50, 83, 81, 50, 82, 81, 83, 50, 84

Does it surprise you to learn that Joe, who receives an A every time he does the work, fails the class with a final average of 47, while Moe, who never scores better than a low B passes with a 73?  You might complain that it is unfair to assume Moe will score a 50 for “junk,” but I disagree. Most faculty are quite generous with partial credit, but even the most lenient will not give you points for work you do not submit.

The moral of this academic incarnation of the race between the tortoise and the hare is that “junk on time” beats flashes of brilliance. Whether you are a student or a professional, always meet deadlines, even when you are not proud of the result. Hold your nose, submit, and pledge to start earlier the next time.

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Transitioning Back to the Faculty https://sites.temple.edu/geophysics/2022/12/27/transitioning-back-to-the-faculty/ https://sites.temple.edu/geophysics/2022/12/27/transitioning-back-to-the-faculty/#respond Wed, 28 Dec 2022 03:16:14 +0000 https://sites.temple.edu/geophysics/?p=982 Continue reading ]]> Looking Back

My final year as Director of General Education (GenEd) has been a busy one and I have fallen behind on my blog posts. After five years as director, I feel a sense of satisfaction — that I’ve made some worthwhile improvements: introducing Course Coordinators to bring consistency to large, multi-section GenEd courses; freshening the inventory by launching “Limited Edition” GenEd courses; and, encouraging a data-driven approach to decision making, including the introduction of dashboards to make the data more accessible.

Flaws remain in Temple’s GenEd program, unsurprising when you consider it launched in 2008 — 15 years ago. Just to give one example, the waiver system put in place when GenEd was created exempts science majors from GenEd Science & Technology classes, and art and music majors from the GenEd Art, but not political science majors from GenEd US Society, or sociology and anthropology majors from GenEd Human Behavior, although transfer student can use introductory classes in those fields to satisfy their GenEd requirements.

Fixing this and other remaining flaws requires a reappraisal of the entire program. I have called for an external review of Temple’s GenEd program. The self-study is nearly complete; the reviewers will visit Temple in February. The job of working with the faculty and administration to weigh and implement the reviewer’s recommendations will fall to my successor.

Looking Ahead

I return to teaching in Fall 2023, but first — sabbatical! This spring I will devote my time and energy to coming up to speed on the applications of machine learning to geophysics, my research specialty. Machine learning was not “a thing” when I was a graduate student, but the geoscience literature exploded during the five years I was in the administration. I am looking forward to having the time to read papers, complete tutorials, and experiment with applying these tools to my own data sets.

Machine learning techniques can be applied to university data as well. I recommend the book, Big Data on Campus to get a sense of the possibilities, as well as the potential ethical pitfalls. That these methods can be applied both to my scientific research and to finding patterns in university data doubles their appeal to me, because whether working as an administrator or faculty member, I remain deeply committed to the improvement of students’ general education experience at Temple University.

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Temple’s Tiny Libraries https://sites.temple.edu/geophysics/2022/03/30/temples-tiny-libraries/ https://sites.temple.edu/geophysics/2022/03/30/temples-tiny-libraries/#respond Wed, 30 Mar 2022 20:20:13 +0000 https://sites.temple.edu/geophysics/?p=969 Continue reading ]]> Many events in Philadelphia are centered around the one book, one Philadelphia program. To encourage students to attend these events we need to get them to read the book, which in 2022 is Quiara Alegría Hudes’ memoir, My Broken Language. Donnell Powell, director of GenEd’s Philadelphia Experience program (PEX) came up with the idea of installing a series of tiny libraries across Temple’s campus and stocking them with the year’s selection. While initially seeded with the “one book,” these would also act as leave-a-book, take-a-book libraries to promote reading. Donnell commissioned current and former Temple art students to decorate the libraries, turning them into works of art. The Nutshell will soon publish an article with more information.

Photo Credit: Nutshell Photographer

Faculty are encouraged to contribute from their own often over-flowing bookshelves any works they feel would interest students. Drop then into whichever tiny library is convenient. PEX student workers will check that the libraries are stocked, moving books between them as needed.

Photo Credit: Nutshell Photographer

In addition to the stationary tiny libraries, GenEd has purchased a custom book bike to bring a mobile tiny library to wherever student congregate. The bike is actually a tricycle with a large box on the front that opens to into a book display.  Keep an eye open for this tiny library on wheels as soon as the weather warms!

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