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Dear honorable members of the CAA Steering Committee,

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With this letter, we would like to express our intention to establish a CAA Special Interest Group for Scientific Scripting Languages in Archaeology (SIG-SSLA) under the auspices of the CAA. The idea for this SIG was developed in 2018 in a session on R as an archaeological tool. Out of this event and the resulting discussions, it was proposed to form such a Special Interest Group to create a permanent platform for the exchange and discussion of ideas and to develop the practical use of R for archaeological applications. After further discussions with colleagues, it became clear that it would be a good idea to extend the focus to all scientific script languages.

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Consequently, a well-attended and constitutive round table meeting took place in Krakow at CAA 2019 (S03 Roundtable Scientific Scripting Languages in Archaeology - Limits and Opportunities of Open Research). At this meeting, a statement of purpose was presented and discussed. The SIG already exists de facto with a Google mailing list (https://groups.google.com/forum/#!forum/scientific-scripting-languages-in-archaeology), a Github organization (https://github.com/sslarch) and its active members (currently 14). This group is currently coordinated by Sophie C. Schmidt, Martin Hinz and Clemens Schmid.

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For the CAA 2020, we would now like to propose to formally include this SIG in the canon of the SIGs of the CAA.

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Statement of purpose

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The purpose of the CAA Special Interest Group Scientific Scripting Languages in Archaeology is to promote the use of scripting languages in archaeology to better align the practice of archaeology with the goals of archaeological science. We will provide an exchange platform for scientists in and around archaeology who use scripting languages to conduct major or minor parts of their research. Scientific programming in non-scripting languages is not excluded, but this SIG focussed on software projects and data analysis work-flows that use code interactively.

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The Special Interest Group is an open format that is intended to support discussion, the circulation of new ideas, and the integration of different approaches in connection with the objectives. Everyone may participate on equal terms following the Ethics Policy of CAA International. To ensure expedient and civil exchange, the SIG committee will remove, edit, or reject comments, commits, code, issues, and other contributions that are not aligned with this policy. To be as inclusive as possible and also for the sake of reproducibility we strongly prefer open-source over proprietary software.

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We especially invite students and young career researches to become part of a wider network of developers and users to improve their skills and promote the use of scripting languages in research, publication and teaching in archaeology. Open and reproducible research is becoming increasingly important in all scientific disciplines. We have to avoid a “lost” generation of students in archaeology that can’t keep pace with this development due to a lack of hard knowledge about computational tools and data exchange standards. The SIG aims to establish the career path of the research software engineer in archaeology.

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Scripting languages

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A scripting language is a programming language which allows live coding interaction with a software interpreter to perform tasks with data. It does not require the compilation of a software module (or only requires this incidentally to the main coding activity) and it is therefore linked to a rapid development style especially suitable for scientific data exploration, analysis, and visualisation. The following list includes popular scripting languages in archaeology and many other sciences:

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  • R
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  • Python
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  • Bash
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  • Netlogo
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  • Stan
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  • OxCal
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  • Observable (JavaScript)
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The scopes and purposes of these scripting languages are highly different. Some of them (like R or Python) are fully capable programming languages which provide methods and libraries for all kind of cross-platform system- and network-interaction. Some (like OxCal) are rather specific collections of basic commands to control individual software tools and therefore serve as mere interfaces. Despite these differences, both kinds of scripting languages allow to create a reproducible representation of a scientific task.

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Reproducible research

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The use of scripting languages for research allows the user to document every necessary step in a research pipeline. The resulting script can be used to reproduce the data analysis by other researchers, given that also the input datasets are provided and – if necessary – the required software environment can be emulated. Scripting languages are therefore the ideal for reproducible research. R and Python, for example, provide specialised frameworks to combine data, code and text (R Markdown, Jupyter Notebooks, …).

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Reproducible research is important for archaeology because it allows other researchers to verify published findings, to easily extend new methods to other datasets and to continue development on available code.

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Some additional conditions to make this process as open and fair as possible are good code documentation, the attribution of software licenses to published code, the creation of stable releases with digital object identifiers (DOIs) and software citation in publications. Code should be equally important as publications. That also means that code generally should be subject to a scientific reviewing process.

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Version control

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Reproducible research ideally also documents the science production process with all inductive and deductive steps of hypothesis building. A modern and powerful way to store a commented succession of changes in text and scripted data analysis is available with tools like Git or SVN which were initially designed for software development. They provide a simple environment to keep track of even minor changes, go back to earlier working stages and allow for well-documented collaborations thanks to forking. The combination of scripting languages and version control is an important basis for a fully comprehensible research process.

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Objectives of the SIG SSLA

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If you approve the formation of this SIG, we would also like to ask you if and how the SIG could get a short slot in the schedule of the CAA2020 conference in Oxford to discuss the organizational affairs among new and established members.

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Thank you for considering this proposal.

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Best regards,

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Sophie C. Schmidt, Martin Hinz and Clemens Schmid

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+ + + + + + + + + + + + + + + diff --git a/hackathon.html b/hackathon.html index c2398d3..6daf7ee 100644 --- a/hackathon.html +++ b/hackathon.html @@ -1,18 +1,17 @@ - + - -hackathon.utf8.md +hackathon.utf8 @@ -235,6 +234,7 @@ border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { diff --git a/hackathonII.Rmd b/hackathonII.Rmd index fb28dab..6dda206 100644 --- a/hackathonII.Rmd +++ b/hackathonII.Rmd @@ -21,10 +21,8 @@ *Clemens Schmid, Martin Hinz* -### Organisational information +**Update: As CAA2020 is [not going to take place](https://caa-international.org/2020/06/11/caa-2020-cancelled/) this session will not happen either. We will think about the concept and may resubmit for CAA 2021.** -**When:** Details unkown -**Where:** Details unkown **Pre-session discussion:** https://github.com/sslarch/caa2020_hackathon/issues ### Abstract diff --git a/hackathonII.html b/hackathonII.html index b1cd4f1..50c1dd6 100644 --- a/hackathonII.html +++ b/hackathonII.html @@ -1,18 +1,17 @@ - + - -hackathonII.utf8.md +hackathonII.utf8 @@ -235,6 +234,7 @@ border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { @@ -349,12 +349,8 @@

S27 CAA Scripting Languages Hackathon II – Unconference!

Clemens Schmid, Martin Hinz

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Organisational information

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When: Details unkown
-Where: Details unkown
-Pre-session discussion: https://github.com/sslarch/caa2020_hackathon/issues

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Update: As CAA2020 is not going to take place this session will not happen either. We will think about the concept and may resubmit for CAA 2021.

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Pre-session discussion: https://github.com/sslarch/caa2020_hackathon/issues

Abstract

Scientific scripting languages are a very powerful tool for scientists to translate research questions and quantitative analysis into a machine-readable, executable and thus reproducible form. In order to promote and support their dissemination to the archaeological community, we have de facto established the Special Interest Group for Scientific Scripting Languages in Archaeology at CAA2019 in Krakow. To celebrate the de jure affiliation of this SIG to the CAA organization in 2020, this session will provide an open hackerspace for users of scripting languages.

diff --git a/index.html b/index.html index 4fd0520..d987ef9 100644 --- a/index.html +++ b/index.html @@ -1,18 +1,17 @@ - + - -index.utf8.md +index.utf8 @@ -235,6 +234,7 @@ border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { diff --git a/protocol_repo.html b/protocol_repo.html index 9fe6c0f..1866669 100644 --- a/protocol_repo.html +++ b/protocol_repo.html @@ -1,18 +1,17 @@ - + - -protocol_repo.utf8.md +protocol_repo.utf8 @@ -235,6 +234,7 @@ border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { diff --git a/round_table.html b/round_table.html index b067e0d..3fe616d 100644 --- a/round_table.html +++ b/round_table.html @@ -1,18 +1,17 @@ - + - -round_table.utf8.md +round_table.utf8 @@ -235,6 +234,7 @@ border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li { diff --git a/site_libs/navigation-1.1/codefolding.js b/site_libs/navigation-1.1/codefolding.js index 8cb6311..8d38a8e 100644 --- a/site_libs/navigation-1.1/codefolding.js +++ b/site_libs/navigation-1.1/codefolding.js @@ -22,8 +22,8 @@ window.initializeCodeFolding = function(show) { // create a collapsable div to wrap the code in var div = $('
'); - if (show || $(this)[0].classList.contains('fold-show')) - div.addClass('in'); + show = (show || $(this).hasClass('fold-show')) && !$(this).hasClass('fold-hide'); + if (show) div.addClass('in'); var id = 'rcode-643E0F36' + currentIndex++; div.attr('id', id); $(this).before(div); diff --git a/statement.html b/statement.html index fc4062e..5ca8696 100644 --- a/statement.html +++ b/statement.html @@ -1,18 +1,17 @@ - + - -statement.utf8.md +statement.utf8 @@ -235,6 +234,7 @@ border: none; display: inline-block; border-radius: 4px; + background-color: transparent; } .tabset-dropdown > .nav-tabs.nav-tabs-open > li {