Software

Barrio Map offers fundamental functionalities like finding locations by conducting searches or selecting coordinates. Users can select from predefined scales and export the scaled maps to particular page sizes. Maps generated using Barrio Map are formal descriptions of particular sites with defined values of resolution, scales, and explicit information on distances. Barrio Map, in conjunction with OpenStreetMaps, is written in R, with functionalities largely leveraged from packages such as Leaflet and Shiny.

CityComp is a Shiny app developed to support the use of the comparative framework developed in Arechiga et al. (2023). In the app, users can directly visualize the results presented in the same paper. Specifically, a graphical and interactive version of Fig. 6 in the same paper is presented in the app. Users can further define a target city and estimate their similarity to cities across the globe. Dynamic filtering and mapping are implemented within the app.

BayClump is a Shiny Dashboard application that is associated with the bayclumpr R package. All the functions implemented in BayClump are sourced from bayclumpr. We eveloped BayClump to allow users with less coding experience to be able to access standarized resources to calibrate and derive reconstructions using clumped isotope datasets.

Enhannced PPE2 is a Human-Machine Interface (HMI) tailored for real-time object detection, with a specific focus on hard hat compliance monitoring in industrial settings. Although this project is tailored for hard hat compliance monitoring, the modular architecture allows easy adaptation for other applications like gengeral PPE detection including masks, goggles, vest and so on. This project focuses on developing the UI associated to the ML model detection algorithm.

This Neural Network-based tool facilitates extraction of building facade color patterns from Google Street View Images.

Salphycon is a shiny app that extends the functionalities of the (phruta) R package. Salphycon is able to (1) find potentially (phylogenetically) relevant gene regions for a given set of taxa on GenBank, (2) retrieve gene sequences and curate taxonomic information from the same database, (3) combine downloaded and local gene sequences, and (4) perform sequence alignment, phylogenetic inference, and basic tree dating tasks. Both phruta and salphycon are focused on species-level analyses.

This is a basic shiny dashboard to perform pairwise comparison of different file submissions. The app is intended to help identify instances of potential plagiarism in coding-based assignments.

Polapp is a live polling platform designed for conferences, events, workshops, meetings, and similar events. Admins can create unique rooms, design questions, and enable access for attendees via unique tokens. Attendees can suggest answers and vote in real-time. Admins can manage questions, voting settings, and get summary statistics.

This tool predicts Escherichia coli (E. coli) levels in the Upper Santa Cruz River using a model trained on public data from 2009-2022. It is intended as a warning of possible high bacterial loads; water quality must still be verified using coliform testing procedures to ensure public safety.

This research is being conducted with the following goals in mind:

• Facilitate evolutionary genomic analysis in the eukaryotic domain
• Make public genomic data more accessible by increasing information content per unit volume of data
• Develop improved methods and algorithms for genome informatics
• Streamline downstream analyses in genomic workflows
• Analyze patterns of genome evolution during the process of adaptation, speciation, diversification and domestication

autogradeR is expected to help instructors grade pre-defined assignments using a particular and relatively simple set of functions. Authograder generates basic templates that can only be accessed by instructors using a pre-defined encrypted password. The current release is based on RMarkdown files.

bayclumpr is a self-contained R package that supports the use of Bayesian models and the analytical framework developed in Román-Palacios et al. (2022) for clumped isotope calibration, temperature reconstructions, and facilitatation of comparisons on Bayesian and classical models. bayclumpr fits both frequentist and Bayesian linear regressions to calibration datasets and performs temperature reconstructions under both frameworks.

The phruta R package is designed to simplify the basic phylogenetic pipeline. All the code is run within the same program and data from intermediate steps are saved in independent folders (optional). phruta retrieves gene sequences, combines newly downloaded to local gene sequences, performs sequence alignments, and basic phylogenetic inference.

The data.table package enables high-performance extended functionality for data tables in R. treedata.table is a wrapper for data.table for phylogenetic analyses that matches a phylogeny to the data.table, and preserves matching during data.table operations.

Bayesian Additive Regression Networks. We apply Bayesian Additive Regression Tree (BART) principles to training an ensemble of small neural networks for regression tasks. Using Markov Chain Monte Carlo, Bayesian Additive Regression Net- works (BARN) samples from the space of single hidden layer neural networks that are conditioned on their fit to data. You can find more information in barnpy and its associated documentation