28th regular meeting

? ppl attended

Open exchange

  • new paper by Clemens:
    • https://github.com/nevrome/mobest.analysis.2022: uses ancient genomic data to reconstruct where people may have come from
    • Clemens tried to make it reproducible, but that’s difficult with high computation set ups, some of the submission scripts will probably be re-written for other set ups
    • is a meta analysis, therefore no problem with big data accessibility –> only links to other data sets
    • data is shared by a lab in Harvard, so hoping the data will be available for the foreseeable future (copying the data may be difficult for legal reasons)
    • maybe the data will be later made accessibly more openly (cooperation coming up)
    • all analysis is written in R, some Haskell is for management of computational pipeline (Haskell shake, similar to R targets), and some more command line tools
  • changing APIs can be a problem for reproducibility
  • Thomas Huet: tries to set up a Workflow with google maps and asks for recommendation
    • extract spatial data from remote sensing, to get a learning data set for machine learning
    • R gee package or ee by Python?
      • Python is used by more people
      • Python is especially useful for spatial analysis (most GIS is written in Python), R would work also, though
      • Pyhton environments is more hard to set up
      • machine learning part is probably also written in Python so maybe better stay with one language
  • deep learning workshop at CAA is booked out
  • there was an R-workshop in Pisa (Francesco Carrer and Joe Roe): good feedback, probably will take place next year again (this was the fourth time already)
    • if you have students that need an R intro
  • archaeovis-package by Sebastien Plutniak: https://github.com/sebastien-plutniak/archeoviz
    • mostly for x-y-z projection of data and showing the stratigraphical position of artefacts after excavation
    • tries to make non-scripting people use shiny
    • preprint is submitted: https://zenodo.org/record/7674699
    • is at PCI for review
  • more GUIs for R are being developed
  • in Clemens part of the workshop in Australia: 20-25 ppl attending
    • quite interesting talks, quite theoretical in part, very diverse topics, but always linked to quantitative methods and R scripting in these domains
    • but Clemens just saw a couple of talks
  • software reviews: https://research-squirrel-engineers.github.io/Impuls_SoftwareRezensionen_DGUF/Draft_EN.html
    • “digital reviews” in archaeological advancements
    • PCI offers the possbility to review software
    • peer reviewing software is something else as reviewing software
    • archeoFOSS community: already engaged in this topic?
    • should the SIG engage?
      • if there would be a centralised platform to find other people’s experiences it would be sensible
      • a list of recommendations / reviews might be already useful
      • “lists” of software are already avaiable
      • software is changing all the time: so reviewing would be one step, but it should be starting point of involvement, improvement – make a open source collaboration
      • if done correctly this could be a great way to improve software (otherwise it might be very annoying for the author to be criticesed and not helped to improve)
      • another point might be: making a software more known (also positive for the author)
      • review paper: a paper that says “if you want to do this kindof analysis, you have these options…”, like a survey

teaching materials: current state of affairs

  • https://sslarch.github.io/MapofComputationalArchaeology/
  • new: introductory information added
  • looks great!
  • feature to maybe add: click on the tag and filter for the tag
  • put it on our homepage (link or embed?
  • where on the website
    • under “research output”?
    • or rather on top as its own tab?
    • maybe important links on a side board (but check mobile view: it will go down to the botton)
  • let’s discuss this on the github: issues for the website (also, should you find a problem with the map)
  • topic for next meeting: how to improve our website

Petr Pajdla on Quarto

  • doesn’t replace Rmarkdown (development will be continued) and written text stays markdown
  • Rmd documents should work with Quarto
  • Quarto is a Command Line Interface, more generic than the R dependent Rmarkdown
  • very well written introduction: quarto.org
  • Quarto is build on Pandoc (may be needed to be installed seperately, esp. pandoc-citeproc for citation)
  • Quarto is now shipped with Rstudio (you may be able to use it out of the box)
  • projects workflow:
    • quarto documents (extension qmd)
    • has a similar YAML-header, but can also be seperated as _quarto.yml
      • splitting one project into several documents easier than with bookdown
      • integrates author, name, email, orcid: easier to include than with Rmarkdown
  • publishing:
    • quarto pub hosts slides, etc whatever, every easy to use
    • github pages easy to set up
  • figure captions: now not any more put next to the ```{r
    • this was a bit unwieldy in Rmarkdown if the labels and captions got very long
    • in Quarto same information as a comment #| –> better readable
    • labels need to be fig.xxx for figures and for tables tab.yyy
  • very easy to have a qmd document to become a presentation
  • ::::{.colums} creates a div environment for tables for html
  • revealjs renders to html
  • same code goes to same output in html, PDF and docx <- details needs to be checked for the future
  • css might not be well translated into other outputs, basic text colours will be the same
  • citations work the same as in Rmarkdown (put the bib file and csl in the YAML)
  • works also in visual mode
  • integrating ready made images works the same -> caption{#label}
    • label: “#fig-xxx”
    • reference:"@fig-xxx"
  • check cross-references
  • supports other languages?
    • Python, R, Julia are implemented - can be used in the same document
    • can the community provide kernels to enlargen the pool of supported languages?
    • knitr or jupyter can be chosen for rendering, thereby using jupyters kernels
    • more languages are supposed to come, if sth is installed on you computer, it should be possible to use
  • Rshiny in Rmarkdown was a great interactive possibility in the documents
    • can be done in Quarto as well
  • example of Quarto used for a course website: https://gia.joeroe.io/ (source at https://github.com/joeroe/gis_in_archaeology)
    • worked really well
  • Petrs Diss uses Quarto: https://github.com/petrpajdla/dataInfrastructures
  • 2 fully funded 1-year MRes (master of research) + 3-year PhD for UK students (or foreign students that obtained their degree in the UK) at Newcastle University.
    • (1) Spatial Analysis in Archaeology: “Spatial Analysis and Modelling to Investigate the Historic Character of Landscapes” - supervisor Francesco Carrer, co-supervisor Sam Turner, industrial partner Historic England; knowledge of GIS essential, knowledge of R or Python desirable.
    • (2) Mathematical Archaeology: “Spatiotemporal modelling of Alpine agricultural revolution” - supervisor: Andrew Baggaley (Maths), co-supervisor Francesco Carrer, industrial partner Dolomiti National Park; experience with techniques for finding both numerical and analytic solutions to differential equations essential, working knowledge of Python or Fortran.
    • For more information, get in touch (francesco.carrer@newcastle.ac.uk) and check the website (https://geospatialcdt.ac.uk/studentship-projects/)

next we will meet at the CAA, more info (where and when) will be distributed on Slack

  • to be discussed:
    • Mastodon and Matrix
    • how to improve on our websit
  • May: talk on morphometrics
  • June: Zach offers to introduce LaTeX

Scientific Scripting Languages in Archaeology

A special interest group of CAA International dedicated to scientific scripting languages in archaeology.


2023-03-01