dyerlab -

The Dyer laboratory is a research lab at Virginia Commonwealth University that focuses on developing and testing tools to aid in understand how landscape features influence genetic connectivity. This requires a mix of theory development, software creation, and evaluation using (largely) non-model systems in the field.

Pollen Movement

Developing models and applications of how to quantify how landscape features, structure, and architecture impacts real-time pollen mediated gene flow in temprate tree species.

Administravia

Developing software to aid in the planning, implementation, and monitoring of data-driven curricular change for academic units.

Conservation Genetics

Range-wide assessment of standing genetic structure in spotted turtles with derivative applications to watershed-level assignment of animals confiscated from the illegal trade.

Recent Blog Posts

FOTJ in the AppStore

There are a series of applications/tools that I’ve been developing in my off that are reaching the point of deployment. The first, FOTJ, is an appliation focused on helping develop Belonging, Participation, and Teamwork in STEM-field courses and has just be released to deploy in a course this summer.

Characteristics of Successful Academic Leadership

Academic leadership requires a unique blend of skills and qualities. Here are some key traits that I associate with leaders who have had transformational impacts on their units, faculty, students, and academic programs.

Population Graphs on Vision Pro

Just got the Apple Vision Pro and started working on laying out using RealityKit. It is a bit different than SceneKit, but both better and more integrated with the features that I’ve come to love about modern Swift + SwiftUI development. I’m very excited.

Spring Semester Faculty Meeting

This first facutly meeting has some input from the National Scholarship Office, the first meeting with our Faculty Training Consultant (this year will focus on Assessment Tools), introduces some proposed changes in CORE curriculum, and opens up a larger discussion on the recent discussion with the Provost about the reorganization and dissolution of our unit.

2024 A Year for Tool Deployment

This is the time of the year to reconfigure and figure out what is on the front burner for 2024! Finals are (finally) finished, projects are wrapping up for the year, and the university is going into the short torpor that allows the passing of the calendar year before rushing into the spring semester. So here are some of my intentions for 2024 from the Dyerlab.

ENVS 543 Narrative

This is a collection of each section narrative I developed for this semsesters ENVS 543: Environmental Data Literacy course, the introduction to R and data manipulation for all incoming graduate students.

Spotted Turtel Assignment Presentation

This is a short presentation that I gave to several state managers about the spotted turtle genetic assignemnt data and interface that I made to help them make decisions on how/if/where animal relocation should proceed.

Population Graphs Re-Incarnated

At long last my administration duties have been satiated and there is a little time to prioritieze my research activities. Time to FINALLY get the popgraph network analysis software out and ready so that in the near future, we can extend that to the Chromosome Walking algorithms…

Student Orientation

A key process in developing and expanding our academic programs in VCU Life Sciences broadly, and the Center for Environmental Studies specifically, is recruitment. This time of year, new students and their families are looking at options for their graduating seniors and it is critical that we are able to show off the opportunities that exist in our units. Here are the slides from this mornings presentations.

Continued Enrollment Increases

Despite the ever present ‘demograhic cliff in college enrollment’ that we continue to prepare for, enrollment in courses offered by the Center for Environmental Studies continues to increase.

Coagulating Samples By Hydrologic Units; or
‘How I learned to HUC my data…’

It is not uncommon in data analysis to need to coagulate samples together based upon some spatial feature of your landscape. Here is an example of how I did this for some spotted turtle sampling locations based upon hydrologic units.

Emydine Conservation Symposium

I had the privilege of being invited up to Juniata College in Huntingdon Pennsylvania to give a talk at the 3rd Emydine Conservation Conference about the work we’ve been doing on Spotted turtles. Here are my slides.

gstudio 1.6.0

Now that the semester is over, I was able to push some new updates out for gstudio. These are some bug fixes and a few new functionalities.

Population Assignment for Confiscated Spotted Turtles

Here is the interface for a population assignment app that I made for some confiscated spotted turtles as part of a larger conservation project.

ENVS Presenatation at VCESS

I got the opportuntity to go out and visit the new Varina Center for Environmental Studies and Sustainabilty and meet with the students and facutly. Very exciting to have a new program so close to the Center.

Full Data Run

I reran the 5% mapping data, keeping all sites with greater than 3 individuals in them, through freebayes. This last SNP calling finished on Feb 24 10:37:29 EST 2023 yielding a potential of 19,879 identified sites across 1318 individuals. This includes all the base individuals, all the confiscated individuals, and the extra sampels that were added to the analysis from the western portion of the species range. There are some samples that did not process correctly, I think I may need to remap these individuals and throw them in with the few smaller singleton sites. I’ll start this today and should be finished by Monday. However, this is a good start on what we are needing.

Removing .DS_Store

Working with .git on Mac will always result in those pesky .DS_Store files that the OS uses to keep track of folder related metadata. Here are two things you need to do to make sure they do not pollute your repositories.

First Filtering Pass for SNP Calling

So I ran a quick and dirty assembly from all the separate parts and then merged individual VCF files to get a first view of how things are sorting out.

Run FreeBayes, Run!!

OK, I’ve run a few tests on calling and several have failed. Here is how I’m going to finsih up and call SNPs for the last 1000 samples.

Running freebayes

Now we need to start calling more SNPs on the indiviudals that have been mapped to the reference genome. I’m breaking this up into groups of individuals (200-300) across many populations. I’m also submitting this via sbatch rather than spinning up a srun /bin/bash approach… Failed.

Pre-Processing Bam Files 🐢

Before doing a large SNP calling exercise, I needed to sort and index all the BAM files that we’ll be working with.

Scrolling Back using ‘Screen’

Tired of attempting to scroll back in your terminal and only getting a list of historical commands when in screen? Here is how to fix it.

Using R on VSCode Remotely

Analyzing SNP data remotely on a server for demultiplexing, etc. can be a bit of a hastle if you would like to do some R analyses. Here is how I set up VSCode to run on my office machine (& laptop) and interface with our servers where all the data are analyzed. I would love to have RStudio be able to do this but, alas, it is not possible yet.

Variant Filtering

So I have a few VCF files that have been mapped and I wanted to take a look at the data. Here is some information on how that has come along thus far. I’m still trying to determine if we are doing the right thing by chunking up the data and the consequences of doing it this way. That being said, here is some information on what we have. This is based upon

Reset Github User for Push

There are times when you need to have multiple different repository accounts for github and moving between them can be a bit of a problem. Here is my solution.

Turtle ddRADSeq Project

This is an ongoing summary of progress on the ddRADSeq project. The beginning of 2023, we finally received the raw sequence data from the provider (total nightmare working with them—they actually lost all my samples). We are now conducting the bioinformatic processing of the data, which is substantial. This page will be updated as we go forward to reflect the current status of the project.

A 5% Representation Run

Scaling back the size of the data to make an assembly to 10% of each individual. **SUCCESS*. Maybe. We recoverded 57,829 contigs from 88,487 sequences.

A 2.5% dDocent Run

This time, we will scale it down to take a random set of 2.5% of each individual’s reads, create new individual files, and then run dDocent on it to try to generate an assembly. At the end, I was able to get 6,676 contigs assembled.

A 10% dDocent Run

A bit optimistic here but I thought I’d run an assembly with 10% of the data from each individual and see how many configs I could produce. It did run and produced 394,146 contigs from 969,927 sequences. But unfortunately, it was running on all the data to map at 10% and was going to take just too long. So I killed it.

Crashing dDocent with Reduced Representations

So, let’s start with a representation of 10% of all the data we have and see about creating an assembly. TL/DR: It failed because I was taking 10% of each individual and creating a single synthetic individual.

Second dDocent Run

A second swing at the option of doing a run of dDocent with the full dataset. FAILED, though this time it may have been hardware related.

First dDocent Run

So, I’ve got my data demultiplexed. Now, we just need to run an assembler on it and call some SNPs. I should be writing the manuscript by the end of the month.

Right Sizing the Sequences

OK, so we finally received all the data (after the financials office was able to pay the bill) and here it is as a large chunk.

Demultiplexing

Here is where we take apart the large lane files and then sort them into individual files based upon the read barcodes

Resources in Swift Package Manager

I really love the Swift Language for its elegance as well as power under the new Apple Silicon. However, development on snapshots of pre-release XCode can, at times, be a bit problematic. Here is a situation I ran into that took me a bit of time to figure out regarding adding resources to a Swift Package.

ddRADSeq Demultiplexing

Setting up the workflow for processing ddRADSeq can be a total pain in the ass. Here is how I was able to do this on a HPC installation at my university with the least amount of pain.

Irreversibility of Structure & Diversity Statistics

An estimate of the amount of genetic variation in a sampled locale is often based upon the standardized mean divergence in allele frequencies as manifest in statistics such as F_ST and their ilk. While informative, and indeed rooted in the foundations of evolutionary theory, simple abstractions such as these may be insensitive to more nuanced components of genetic structure due to their robustness—it is well understood that a specific value of F_ST may represent an infinite number of population arrangements, all of which just happen to have the same ratio of among to within population genetic variance.

Rendering R Help Files

Included help files are critical for working in R and, despite the pain that is caused by creating them when you make libraries, they are an essential part of the experience and help your users more easily gain proficiency. One of the challenges, however, has been including the actual text of a help file into a markdown document. Here is an example of how to include help files by rendering .Rd to Html and then knitting it into the document itself.

Basic R Data Types

This is a topic for basic data literacy in R that introduces the basic data types used in most analyses.

Markdown in the Classroom

Installing R Packages from Source

There are times when you use install.packages() and it says something like “the package requested cannot be installed on this version of R.” This typically means something like it is an old pacakge or one that has a lot of dependencies that may be problematic. Here is the first thing to try when you get to those situations.

GitHub Personal Access Tokens

GitHub has recently moved over to using Personal Access Tokens for repositories. So I thought it would be a good idea to write out how to configure your setup so that you have RStudio set up and ready to go. This setup will walk you through how to do this so your life will be just a little bit better.

GitHub Classroom

This year I am reconfiguring my teaching to be more granular in scope. Historically, I have made all my quantitative lectures part of a single large GitHub repository, which is good for me. However, this does have a problem that it is getting so large that it may only be good for me and not for anyone else. So, I’ve decided to break up my teaching compoinents into individual, stand-alone, GitHub Repositories & use GitHub Classroom for teaching.

xcrun issues on Ventura Beta

Experiencing some problems with git and odd startup screens on the Terminal.app. Apparently I had to reset the command line tools with the new Xcode-beta. Here is how I fixed it.

Update to the R POPGRAPH library

As part of an ongoing research project, I was simulating some populatiuon graph structures and found an annoying feture in the current popgraph library when comparing disconnected graphs for distance congruence. Fixed it and updated the version to 1.5.3

Github Distill Manuscript Automation

Here is a quick fix to helping you streamline your manuscript creation using the rmarkdown::distill package so that your output is automatically put in the right locations for display on Github Pages.

Workshop on R Data Literacy

The lecture content from a 2-day workshop I delivered for individuals working at the Virginia Department of Environmental Quality tht focused on building a foundation of data analysis using R.

Guest Lecture in ENVS102

Today I delivered a guest lecture to the students in ENVS102: Introduction to Environmental Studies II about my career path, what my reserach is about, and some larger picture issues for the Environmental Studies program.

Guest Lecture in ENVS102

Today I delivered a guest lecture to the students in ENVS102: Introduction to Environmental Studies II about my career path, what my reserach is about, and some larger picture issues for the Environmental Studies program.

Mapping & SNP Calling

This page documents the progress of mapping dempultiplexed sequences from individuals onto our reference genome and calling SNPs.

Unnecessary Output by dplyr

I love tidyverse but cannot understand how the authors disregard meaningless output so poorly. Here is how to quiet some of that extra cruft when you load in tidyverse

Craft.app + rstudio::distill = blogging

As part of my switch from using Hugo + RMarkdown to make my own blogs to using rstudio::distill to increase some of the simplicity that happens in my life—Hugo was just too much complexity and fragility and at times would just break. However, distill is something that I can use to directly integrate into my workflows as well as capture the raw manuscripts I’m working on (distill manuscripts are quite nice and can serve as a pre-print option as well).

Craft + RStudio + Distill = Post

This is the R side of the Craft -> Website through RStudio and Distill. I’ve set up a workflow here to take posts exported in markdown from Craft to be imported into this site’s workflow.

Smoothing rasters

Sometimes it is helpful for visualization purposes (or when making a nice graphic), to smooth out a raster image. Here are some cheap and quick methods.

Moving Old Markdown Posts

Another take at moving old markdown content to a new platform. While markdown is supposed to be universal, the kinds of meta data assocaited with it in certain systems is a bit wonky and forces us to do some magic. Here I take a less retentive approach than what I did moving manuscript entries over since I do not have to maintain as much meta-data about each post.

Moving Manuscripts from Hugo

The use of Markdown for your site is very helpful but not alll markdown formats are the same. Here is how I moved from Hugo to rstudio::distill for the manuscripts section of the lab webpage.

Moving from HUGO to distill

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MacOS Monterey beta

Apple has released the developers version of all its operating systems to be released in the fall. Here is a quick dive into one of them—MacOS Monterey.

Spring 2021 Landscape Genetics Workshop

This spring, my Landscape Genetics Workshop will need to be held virtually via zoom. While that provides a set of unique challenges, it looks like this is facilitating a more diverse group of attendees, which is always beneficial. All course content is hosted on this site under Courses.

Problems with RMarkdown HTMLWidgets

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Obsidian mobile

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Population Graphs Swift Edition

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dplyr summarize Warnings

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Spring 2020 ERAC Meeting Slides

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Setting up PostGIS on GCP

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Setting up Postgresql on mac

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Remferts Dogwood Presentation at the Research Showcase

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Population Graph Stability

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Simulating Random Populations

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The Enigmatic Seedlings Data File

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get map Problems w o Google API

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Landscape Genetics Workshop 2019

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RStudio Server on Ubuntu

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UVa Center for Public Health Genomics

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January CES Faculty Meeting

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Jane Remfert Doctoral Candidate

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Setting up Atom for Pweave Or What the what

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Using Google Drive as an R Data Repository

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Poisonous Plants in the Commonwealth

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The Atom Editor

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CES Curriculum Meeting

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CSBC Faculty Meeting

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CES Faculty Meeting

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ENVS 601 Lecture

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ENVS Welcome Slides

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Capturing contents within Curly Brackets

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CES Fall Semester Faculty Meeting

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Per Hour Population Growth

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VDOT Progress Update

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Thanks Research Gate

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March Faculty Meeting Notes

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ggproblems

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New sequencer

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New URLs

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Bayesian Models

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R Post of the Day

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New Job

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Life Sciences Graduation

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Talk at Temple

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Spatial Data Sources

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Dyer ENVS Research Talk

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ENVS Faculty Meeting

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Applied Environmental Statistics

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Evolution 2016 Youtube Channel

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Collab Slack R

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Google Earth Pro 8211 Now Free

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Google Drive 038 Git

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Landscape Epigenetics

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Evolution 2016 8211 Austin Texas

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PCR Gods

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Intalling Shiny Server on Ubuntu 14 LTS

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Life Sciences Graduation

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Congratulations to Dr Viverette

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RStudio Cheatsheets

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Layered Maps in R Using GGPlot of course 8230

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Point And Click Theme Editing for ggplot

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Congratulations Chitra

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Volume 0 8211 On iBooks Store

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Presentation Zen

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STRUCTURE on OSX

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Cropping Rasters

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Raster Plotting

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Welcome to the Lab Bonnie

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Denver Talk

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ENVS Orientation

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Effective Population Size

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Chapter 2 Hardy Weinberg Equilibrium

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Environmental Studies Orientation

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Prothonotary Warblers

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Chapter 1 Learning R

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New Semester

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Congratulations Anna Tucker

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Applied Population Genetics Textbook Release

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Life Sciences Graduation

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Laboratory Move

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NSF Grant Recommended for Funding

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The Taxonomy of Academic Sustainability

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Eyes on Climate

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A talk at the University of Paris Sud

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Research Talk Chaire EcoConception

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Research Talk Chaire Éco conception

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Methylation Structure

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Installing Gitbook on OSX

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Paris 2015

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Merging data frames

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Compiling RGDAL on OSX 8211 Why do you hate me

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Loading in Rasters

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RVA Urban Dogwood

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Basic graphics in R

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Welcome Jane Remfert

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Dyerlab Temporary Headquarters

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Installing R packages from github

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Compiling the GSL Library for OSX

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Congratulations to Jameson Hinkle

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Hello R Markdown

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Making better presentations

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New Position

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Install rgeos on OSX

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Color palettes in ggpairs

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New Lab Member

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A terrible loss for VCU

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Turning In Assignments via Google Sharing

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Setting Up Your Site for Syndication

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Unix Basics

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Diluting Primers

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Compiling r-devel

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Updating R and With Current Libraries

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Restriction Enzymes for AFLPs

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Dyer’s Philosophy of Life

There are many great intellectual traditions that our species has derived related to a general philosophy of life. Here is mine.