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.

 

Recent Posts

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.
Feb 24, 2023

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.
Feb 23, 2023

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.
Feb 22, 2023

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.
Feb 21, 2023

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.
Feb 21, 2023

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.
Feb 20, 2023

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.
Feb 20, 2023

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.
Feb 20, 2023

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
Feb 17, 2023

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.
Feb 16, 2023

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.
Feb 15, 2023

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.
Jan 31, 2023

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.
Jan 30, 2023

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.
Jan 27, 2023

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.
Jan 25, 2023

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.
Jan 24, 2023

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.
Jan 21, 2023

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.
Jan 20, 2023

Demultiplexing

Here is where we take apart the large lane files and then sort them into individual files based upon the read barcodes
Jan 16, 2023

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.
Oct 28, 2022

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.
Oct 5, 2022

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 FST 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 FST 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.
Sep 30, 2022

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.
Sep 7, 2022

Basic R Data Types

This is a topic for basic data literacy in R that introduces the basic data types used in most analyses.
Sep 6, 2022

Markdown in the Classroom

Today I will be working on…
Sep 1, 2022

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.
Aug 26, 2022

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.
Aug 25, 2022

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.
Aug 24, 2022

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.
Aug 16, 2022

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
Mar 22, 2022

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.
Mar 18, 2022

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.
Mar 4, 2022

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.
Feb 15, 2022

Mapping & SNP Calling

This page documents the progress of mapping dempultiplexed sequences from individuals onto our reference genome and calling SNPs.
Feb 13, 2022

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
Feb 1, 2022

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).
Dec 21, 2021

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.
Dec 21, 2021

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.
Dec 15, 2021

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.
Dec 14, 2021

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.
Dec 13, 2021

Moving from HUGO to distill

A short description of the post.
Jun 11, 2021

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.
Jun 9, 2021

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.
May 23, 2021

Problems with RMarkdown HTMLWidgets

A short description of the post.
Mar 16, 2021

Obsidian mobile

A short description of the post.
Mar 13, 2021

Population Graphs Swift Edition

A short description of the post.
Mar 3, 2021

dplyr summarize Warnings

A short description of the post.
Feb 9, 2021

Spring 2020 ERAC Meeting Slides

A short description of the post.
May 12, 2020

Setting up PostGIS on GCP

A short description of the post.
Mar 19, 2020

Setting up Postgresql on mac

A short description of the post.
Mar 12, 2020

Remferts Dogwood Presentation at the Research Showcase

A short description of the post.
Feb 27, 2020

Population Graph Stability

A short description of the post.
Apr 22, 2019

Simulating Random Populations

A short description of the post.
Apr 21, 2019

The Enigmatic Seedlings Data File

A short description of the post.
Mar 29, 2019

get map Problems w o Google API

A short description of the post.
Mar 25, 2019

Landscape Genetics Workshop 2019

A short description of the post.
Mar 24, 2019

RStudio Server on Ubuntu

A short description of the post.
Mar 8, 2019

UVa Center for Public Health Genomics

A short description of the post.
Feb 13, 2019

January CES Faculty Meeting

A short description of the post.
Jan 25, 2019

Jane Remfert Doctoral Candidate

A short description of the post.
Dec 6, 2018

Setting up Atom for Pweave Or What the what

A short description of the post.
Jul 23, 2018

Using Google Drive as an R Data Repository

A short description of the post.
Jul 19, 2018

Poisonous Plants in the Commonwealth

A short description of the post.
Jul 19, 2018

The Atom Editor

A short description of the post.
Jun 20, 2018

CES Curriculum Meeting

A short description of the post.
Mar 23, 2018

CSBC Faculty Meeting

A short description of the post.
Jan 31, 2018

CES Faculty Meeting

A short description of the post.
Jan 29, 2018

ENVS 601 Lecture

A short description of the post.
Oct 23, 2017

ENVS Welcome Slides

A short description of the post.
Oct 7, 2017

Capturing contents within Curly Brackets

A short description of the post.
Oct 5, 2017

CES Fall Semester Faculty Meeting

A short description of the post.
Sep 1, 2017

Per Hour Population Growth

A short description of the post.
May 22, 2017

VDOT Progress Update

A short description of the post.
May 22, 2017

Thanks Research Gate

A short description of the post.
Apr 17, 2017

March Faculty Meeting Notes

A short description of the post.
Mar 17, 2017

ggproblems

A short description of the post.
Mar 14, 2017

New sequencer

A short description of the post.
Mar 9, 2017

New URLs

A short description of the post.
Mar 2, 2017

Bayesian Models

A short description of the post.
Feb 28, 2017

R Post of the Day

A short description of the post.
Feb 20, 2017

New Job

A short description of the post.
Jan 10, 2017

Life Sciences Graduation

A short description of the post.
Dec 10, 2016

Talk at Temple

A short description of the post.
Nov 13, 2016

Spatial Data Sources

A short description of the post.
Oct 6, 2016

Dyer ENVS Research Talk

A short description of the post.
Oct 3, 2016

ENVS Faculty Meeting

A short description of the post.
Sep 16, 2016

Applied Environmental Statistics

A short description of the post.
Aug 29, 2016

Evolution 2016 Youtube Channel

A short description of the post.
Jul 10, 2016

Collab Slack R

A short description of the post.
Jul 8, 2016

Google Earth Pro 8211 Now Free

A short description of the post.
Jun 25, 2016

Google Drive 038 Git

A short description of the post.
Jun 22, 2016

Landscape Epigenetics

A short description of the post.
Jun 19, 2016

Evolution 2016 8211 Austin Texas

A short description of the post.
Jun 17, 2016

PCR Gods

A short description of the post.
Jun 7, 2016

Intalling Shiny Server on Ubuntu 14 LTS

A short description of the post.
Jun 5, 2016

Life Sciences Graduation

A short description of the post.
May 14, 2016

Congratulations to Dr Viverette

A short description of the post.
Apr 22, 2016

RStudio Cheatsheets

A short description of the post.
Apr 20, 2016

Layered Maps in R Using GGPlot of course 8230

A short description of the post.
Apr 20, 2016

Point And Click Theme Editing for ggplot

A short description of the post.
Apr 12, 2016

Congratulations Chitra

A short description of the post.
Apr 11, 2016

Volume 0 8211 On iBooks Store

A short description of the post.
Apr 8, 2016

Presentation Zen

A short description of the post.
Apr 7, 2016

STRUCTURE on OSX

A short description of the post.
Apr 5, 2016

Cropping Rasters

A short description of the post.
Mar 18, 2016

Raster Plotting

A short description of the post.
Mar 18, 2016

Welcome to the Lab Bonnie

A short description of the post.
Mar 11, 2016

Denver Talk

A short description of the post.
Feb 21, 2016

ENVS Orientation

A short description of the post.
Feb 20, 2016

Effective Population Size

A short description of the post.
Feb 19, 2016

Chapter 2 Hardy Weinberg Equilibrium

A short description of the post.
Feb 5, 2016

Environmental Studies Orientation

A short description of the post.
Feb 3, 2016

Prothonotary Warblers

A short description of the post.
Jan 29, 2016

Chapter 1 Learning R

A short description of the post.
Jan 15, 2016

New Semester

A short description of the post.
Jan 11, 2016

Congratulations Anna Tucker

A short description of the post.
Jan 8, 2016

Applied Population Genetics Textbook Release

A short description of the post.
Dec 17, 2015

Life Sciences Graduation

A short description of the post.
Dec 12, 2015

Laboratory Move

A short description of the post.
Dec 2, 2015

NSF Grant Recommended for Funding

A short description of the post.
Nov 18, 2015

The Taxonomy of Academic Sustainability

A short description of the post.
Oct 29, 2015

Eyes on Climate

A short description of the post.
Sep 28, 2015

A talk at the University of Paris Sud

A short description of the post.
Sep 24, 2015

Research Talk Chaire EcoConception

A short description of the post.
Sep 22, 2015

Research Talk Chaire Éco conception

A short description of the post.
Sep 22, 2015

Methylation Structure

A short description of the post.
Sep 16, 2015

Installing Gitbook on OSX

A short description of the post.
Sep 4, 2015

Paris 2015

A short description of the post.
Sep 4, 2015

Merging data frames

A short description of the post.
Aug 27, 2015

Compiling RGDAL on OSX 8211 Why do you hate me

A short description of the post.
Aug 27, 2015

Loading in Rasters

A short description of the post.
Aug 26, 2015

RVA Urban Dogwood

A short description of the post.
Aug 25, 2015

Basic graphics in R

A short description of the post.
Aug 24, 2015

Welcome Jane Remfert

A short description of the post.
Aug 19, 2015

Dyerlab Temporary Headquarters

A short description of the post.
Aug 4, 2015

Installing R packages from github

A short description of the post.
Jul 30, 2015

Compiling the GSL Library for OSX

A short description of the post.
Jul 29, 2015

Congratulations to Jameson Hinkle

A short description of the post.
Jul 28, 2015

Hello R Markdown

A short description of the post.
Jul 23, 2015

Making better presentations

A short description of the post.
Apr 29, 2015

New Position

A short description of the post.
Apr 16, 2015

Install rgeos on OSX

A short description of the post.
Mar 31, 2015

Color palettes in ggpairs

A short description of the post.
Mar 26, 2015

New Lab Member

A short description of the post.
Mar 26, 2015

A terrible loss for VCU

A short description of the post.
Feb 5, 2015

Turning In Assignments via Google Sharing

A short description of the post.
Jan 23, 2015

Setting Up Your Site for Syndication

A short description of the post.
Jan 21, 2015

Unix Basics

A short description of the post.
Oct 10, 2013

Diluting Primers

A short description of the post.
Sep 14, 2013

Compiling r-devel

A short description of the post.
Jun 3, 2013

Updating R and With Current Libraries

A short description of the post.
Jun 3, 2013

Restriction Enzymes for AFLPs

A short description of the post.
Feb 1, 2013

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.
Oct 14, 1969
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