Virtual Morphometrics Meetup

This is the repository for scripts and other files that we will use for the Virtual Morphometrics meetings.

using pairwise in geomorph (ID)

• Materials from April 29th (using r pairwise() in r RRPP or r geomorph):
  • the r .Rmd file that can be rendered ("knit") for slides or "purl" for just the R code. That link is here
  • the markdown file (rendered to show output) is here
  • Abbreviated and anonymized output from the chat window from the meeting is here

SlicerMorph (MM and team)

• On May 6th,2020 the SlicerMorph team will be doing a short introduction on their tools for 3D scans.
  • The link for materials for this tutorial are here.
  • The SlicerMorph website is here

Introduction to PCM for GMM (DA)

• May 27th, 2020 - Dr. Dean Adams is providing a birds eye view of phylogenetic comparative methods (PCM) in the context of GMM.

  • The link for the r .Rmd file is here. the r .Rmd file that can be rendered ("knit") for slides or "purl" for just the R code. In this case there are some associated images in the PCM-Image folder. So if you are unfamilar with how to clone a git repo, go to the big green button that says "clone or download", download the zipped file, unzip it on your computer, and then open a fresh instance of Rstudio and you should be able to click on the r .Rmd files and they will be able to knit (rendered). You may need to change your working directory if you already had Rstudio open.
  • If you prefer to follow along with the slides, this same repository (that you just downloaded or clones) has a self-contained file PCM-Intro.html that if you have locally on your computer, and click it, it will open a beautiful presentation in your browser.

  -- The chat transcript for this meeting (anonymized) is here in case you wanted to grab the references, etc.

Combining landmark configurations (MC)

• June 17th, 2020: Dr. Michael Collyer Making Heads or Tails of Combined Landmark Configurations in GM data.

  • The link for the r .Rmd file is here. To render this in R studio you will need some associated files so download or clone the repository (see instructions above for this). Please Note that this depends on the most recent version of geomorph (v3.3.1), so you may wish to update geomorph.
  • Alternatively you can use j the self contained .html slides in the repo (just click on the html file after download.)
  • Or just look at it on github here. Please note that github (for some reason) does not support LaTeX formatting so the equations won't look right (they will in the slides or in R studio.)

Introduction to projections for GMM

• July 1st, 2020, Ian Dworkin

• The link for the r .Rmd file is here. You can render this directly. Please Note that this depends on the most recent version of geomorph (v3.3.1), so you may wish to update geomorph. Just download (or even copy and paste the raw file) and hit the knit button!

• Alternatively you can use the self contained .html slides in the repo (just click on the html file after download.)

• I don't recommend using it live on github as it does not render the equations.

August 26th 2020

link to questions for breakout rooms

Other stuff

• ID needs to re-organize this, sorry!

• However feel free to use the files here to help you and help others.