? 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 -> {#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

Advertisement by Francesco Carrer

• 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