Numerical Analysis and Scientific Computing Commons^™

On The Geodesic Centers Of Polygonal Domains, Haitao Wang

Computer Science Faculty and Staff Publications

In this paper, we study the problem of computing Euclidean geodesic centers of a polygonal domain P of n vertices. We give a necessary condition for a point being a geodesic center. We show that there is at most one geodesic center among all points of P that have topologically-equivalent shortest path maps. This implies that the total number of geodesic centers is bounded by the size of the shortest path map equivalence decomposition of P, which is known to be O(n^{10}). One key observation is a pi-range property on shortest path lengths when points are moving. With these observations, …

Bayesian Networks To Assess The Newborn Stool Microbiome, William E. Bennett Jr.

McKelvey School of Engineering Graduate Student Theses & Dissertations

In human stool, a large population of bacterial genes and transcripts from hundreds of genera coexist with host genes and transcripts. Assessments of the metagenome and transcriptome are particularly challenging, since there is a great deal of sequence overlap among related species and related genes. We sequenced the total RNA content from stool samples in a neonate using previously-described methods. We then performed stepwise alignment of different populations of RNA sequence reads to different indices, including ribosomal databases, the human genome, and all sequenced bacterial genomes. Each pool of RNA at each alignment step was subjected to compression to assess …

High Altitude Cosmic Ray Detection, Jordan D. Van Nest

2017 Academic High Altitude Conference

Cosmic rays are high energy atomic nuclei travelling near the speed of light that collide with atoms and molecules in Earth’s upper atmosphere (primarily with nitrogen and oxygen), breaking down into a shower of particles of various energies in the stratosphere. As they travel earthward, these particles continue to break down and lose energy which results in relatively little ionizing radiation reaching the surface. Due to the scattering of cosmic rays, the angle at which the rays enter the atmosphere can affect the number and energies of ionizing particles detected at various altitudes. When using a standard Geiger counter on …

Creating Art Patterns With Math And Code, Boyan Kostadinov

Publications and Research

The goal of this talk is to showcase some visualization projects that we developed for a 3-day Code in R summer program, designed to inspire the creative side of our STEM students by engaging them with computational projects that we developed with the purpose of mixing calculus level math and code to create complex geometric patterns. One of the goals of this program was to attract more minority and female students into applied math and computer science majors.

The projects are designed to be implemented using the high-level, open-source and free computational environment R, a popular software in industry for …

Generalizing The Quantum Dot Lab Towards Arbitrary Shapes And Compositions, Matthew A. Bliss, Prasad Sarangapani, James Fonseca, Gerhard Klimeck

The Summer Undergraduate Research Fellowship (SURF) Symposium

As applications in nanotechnology reach the scale of countable atoms, computer simulation has become a necessity in the understanding of new devices, such as quantum dots. To understand the various optoelectronic properties of these nanoparticles, the Quantum Dot Lab (QDL) has been created and powered by NEMO5 to simulate on multi-scale, multi-physics bases. QDL is easy to use by offering choices of different QD geometries such as shapes and sizes to the users from a predefined menu. The simplicity of use, however, limits the simulation of general QD shapes and compositions. A method to import generic strained crystalline and amorphous …

Analyzing Sports Training Data With Machine Learning Techniques, Rehana Mahfuz, Zeinab Mourad, Aly El Gamal

The Summer Undergraduate Research Fellowship (SURF) Symposium

In the sports industry, there has not been enough effort in analyzing the personalized monitoring data of athletes collected during training sessions. This research is an attempt to find meaningful patterns in the Purdue Women’s Soccer training data that could help the coach design more efficient training sessions. We are specifically interested in studying this problem as an unsupervised learning problem. Our initial attempt is to cluster the players as well as drills into groups using k-means, c-means and spectral clustering algorithms, combined with feature transformation and reduction steps. These basic algorithms serve as a benchmark to measure performance improvements …

Density Functional Theory Based Electrolyte Design Formulation For Lithium-Sulfur Batteries, Cynthia Ly, Carolyn Sturges, Vijay Murugesan

STAR Program Research Presentations

Lithium-ion (Li-ion) batteries are commonly used in portable electronics such as cellphones and laptops. Most Li-ion batteries operate on intercalation principle with typical theoretical specific energy of 400-600 (Wh/Kg). There is great scientific interest in lithium-sulfur (Li-S) batteries as a possible successor of traditional Li-ion batteries because Li-S holds the potential of being a very powerful (1550 Wh/kg theoretical specific energy) yet very cost-efficient battery (due the abundance and inexpensiveness of sulfur). However, one major problem in Li-S battery research is the polysulfide “shuttle phenomenon”, which is the shuttling of polysulfide species due to the dissolution of sulfide from the …

Changes In R, R Core Team

The R Journal

CHANGES IN R 3.3.1 patched

CHANGES IN R 3.3.1

CHANGES IN R 3.3.0

Changes On Cran, Kurt Hornik, Achim Zeileis

The R Journal

In the past 8 months,1322 new packages were added to the CRAN package repository. 43 packages were unarchived,48 archived,1 package had to be removed.The following shows the growth of the number of active packages in the CRAN package repository:

Nonparametric Tests For The Interaction In Two-Way Factorial Designs Using R, Jos Feys

The R Journal

An increasing number of R packages include nonparametric tests for the interaction in two-way factorial designs. This paper briefly describes the different methods of testing and reports the resulting p-values of such tests on datasets for four types of designs: between, within, mixed, and pretest-posttest designs. Potential users are advised only to apply tests they are quite familiar with and not be guided by p-values for selecting packages and tests.

Using Decipher V2.0 To Analyze Big Biological Sequence Data In R, Erik S. Wright

The R Journal

In recent years, the cost of DNA sequencing has decreased at a rate that has outpaced improvements in memory capacity. It is now common to collect or have access to many gigabytes of biological sequences. This has created an urgent need for approaches that analyze sequences in subsets without requiring all of the sequences to be loaded into memory at one time. It has also opened opportunities to improve the organization and accessibility of information acquired in sequencing projects. The DECIPHER package offers solutions to these problems by assisting in the curation of large sets of biological sequences stored in …

Scmamp: Statistical Comparison Of Multiple Algorithms In Multiple Problems, Borja Calvo, Guzmán Santafé

The R Journal

Comparing the results obtained by two or more algorithms in a set of problems is a central task in areas such as machine learning or optimization. Drawing conclusions from these comparisons may require the use of statistical tools such as hypothesis testing. There are some interesting papers that cover this topic. In this manuscript we present scmamp, an R package aimed at being a tool that simplifies the whole process of analyzing the results obtained when comparing algorithms, from loading the data to the production of plots and tables.

Comparing the performance of different algorithms is an essential step …

Swmpr: An R Package For Retrieving, Organizing, And Analyzing Environmental Data For Estuaries, Marcus W. Beck

The R Journal

The System-Wide Monitoring Program (SWMP)was implemented in 1995 by the US National Estuarine Research Reserve System. This program has provided two decades of continuous monitoring data at over 140 fixed stations in 28 estuaries. However, the increasing quantity of data provided by the monitoring network has complicated broad-scale comparisons between systems and, in some cases, prevented simple trend analysis of water quality parameters at individual sites. This article describes the SWMPr package that provides several functions that facilitate data retrieval, organization, and analysis of time series data in the reserve estuaries. Previously unavailable functions for estuaries are also provided to …

Spatio-Temporal Interpolation Using Gstat, Benedikt Gräler, Edzer Pebesma, Gerard Heuvelink

The R Journal

We present new spatio-temporal geostatistical modelling and interpolation capabilities of the R package gstat. Various spatio-temporal covariance models have been implemented, such as the separable, product-sum, metric and sum-metric models. Inareal-world application we comparespatio temporal interpolations using these models with a purely spatial kriging approach. The target variable of the application is the daily mean PM10 concentration measured at rural air quality monitoring stations across Germany in 2005. R code for variogram fitting and interpolation is presented in this paper to illustrate the workflow of spatio-temporal interpolation using gstat. We conclude that the system works properly and that the …

Model Builder For Item Factor Analysis With Openmx, Joshua N. Pritikin, Karen M. Schmidt

The R Journal

We introduce a shiny web application to facilitate the construction of Item Factor Analysis (a.k.a. Item Response Theory) models using the OpenMx package. The web application assists with importing data, outcome recoding, and model specification. However, the app does not conduct any analysis but, rather, generates an analysis script. Generated Rmarkdown output serves dual purposes: to analyze a data set and demonstrate good programming practices. The app can be used as a teaching tool or as a starting point for custom analysis scripts.

Quickpsy: An R Package To Fit Psychometric Functions For Multiple Groups, Daniel Linares, Joan López-Moliner

The R Journal

quickpsy is a package to parametrically fit psychometric functions. In comparison with previous R packages, quickpsy was built to easily fit and plot data for multiple groups. Here, we describe the standard parametric model used to fit psychometric functions and the standard estimation of its parameters using maximum likelihood. We also provide examples of usage of quickpsy, including how allowing the lapse rate to vary can sometimes eliminate the bias in parameter estimation, but not in general. Finally, we describe some implementation details, such as how to avoid the problems associated to round-off errors in the maximisation of the …

Variable Clustering In High-Dimensional Linear Regression: The R Package Clere, Loïc Yengo, Julien Jacques, Christophe Biernacki, Mickael Canouil

The R Journal

Dimension reduction is one of the biggest challenges in high-dimensional regression models. We recently introduced a new methodology based on variable clustering as a means to reduce dimensionality. We present here the R package clere that implements some refinements of this methodology. An overview of the package functionalities as well as examples to run an analysis are described. Numerical experiments on real data were performed to illustrate the good predictive performance of our parsimonious method compared to standard dimension reduction approaches.

Maps, Coordinate Reference Systems And Visualising Geographic Data With Mapmisc, Patrick E. Brown

The R Journal

The mapmisc package provides functions for visualising geospatial data, including fetching background map layers, producing colour scales and legends, and adding scale bars and orientation arrows to plots. Background maps are returned in the coordinate reference system of the dataset supplied, and inset maps and direction arrows reflect the map projection being plotted. This is a “light weight” package having an emphasis on simplicity and ease of use

Editorial, Michael Lawrence

The R Journal

On behalf of the editorial board, I am pleased to publish Volume 8, Issue 1 of the R Journal. This issue contains 27 contributed research articles. Each of them either presents an R package, a specific extension of an R package or applications using R packages available from the Comprehensive R Archive Network (CRAN, http:://CRAN.R-project.org). It thus provides a small but current cross-section of the burgeoning R ecosystem.

Metaplus: An R Package For The Analysis Of Robust Meta-Analysis And Meta-Regression, Ken J. Beath

The R Journal

The metaplus package is described with examples of its use for fitting meta-analysis and meta-regression. For either meta-analysis or meta-regression it is possible to fit one of three models: standard normal random effect, t-distribution random effect or mixture of normal random effects. The latter two models allow for robustness by allowing for a random effect distribution with heavier tails than the normal distribution, and for both robust models the presence of outliers may be tested using the parametric bootstrap. For the mixture of normal random effects model the outlier studies may be identified through their posterior probability of membership in …