|Id||Title||Authors||Abstract||Picture||Thematic fields▲||Recommender||Reviewers||Submission date|
30 Sep 2022
Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF dataBharath Nair, Ismael Rodríguez Palomo, Bo Markussen, Carsten Wiuf, Sarah Fiddyment and Matthew Collins https://doi.org/10.1101/2022.03.13.483627
Assessing glutamine deamination in ancient parchment samplesRecommended by Beatrice Demarchi based on reviews by Maria Codlin and 3 anonymous reviewers
Data authenticity and approaches to data authentication are crucial issues in ancient protein research. The advent of modern mass spectrometry has enabled the detection of traces of ancient biomolecules contained in fossils, including protein sequences. However, detecting proteins in ancient samples does not equate to demonstrating their endogenous nature: instead, if the mechanisms that drive protein preservation and degradation are understood, then the extent of protein diagenesis can be used for evaluating preservational quality, which in turn may be related to the authenticity of the protein data.
The post-mortem deamidation of asparaginyl and glutamyl residues is a key degradation reaction, which can be assessed effectively on the basis of mass spectrometry data, and which has accrued a long history of research, both in terms of describing the mechanisms governing the reactions and with regard to the best strategies for assessing and quantifying the extent of glutamine (Gln) and asparagine (Asn) deamidation in ancient samples (Pal Chowdhury et al., 2019; Ramsøe et al., 2021, 2020; Schroeter and Cleland, 2016; Simpson et al., 2016; Solazzo et al., 2014; Welker et al., 2016; Wilson et al., 2012).
In their paper, Nair and colleagues (2022) build on this wealth of knowledge and present a tool for quantifying the extent of Gln deamidation in parchment. Parchment is a collagen-based material which can yield extraordinary insights into manuscript manufacturing practices in the past, as well as on the daily lives of the people who assembled and used them (“biocodicology”) (Fiddyment et al., 2021, 2019, 2015; Teasdale et al., 2017). Importantly, the extent of deamidation can be directly related to the quality of the parchment produced: rapid direct deamidation of Gln is induced by the liming process, therefore high extents of deamidation are linked to prolonged exposure to the high pH conditions which are typical of liming, thus implying lower-quality parchment.
Nair et al.’s approach focuses on collagen peptides which are typically detected during MALDI-TOF mass spectrometry analyses of parchment and build a simple three-step workflow able to yield an overall index of deamidation for a sample (the parchment glutamine index - PQI) 一 taking into account that different Gln residues degrade at different rates according to their micro-chemical environment. The first step involves pre-processing the MALDI spectra, since Nair et al. are specifically interested in maximising information which can be obtained by low-quality data. The second step builds on well-established methods for quantifying Q → E from MALDI-TOF data by modelling the convoluted isotope distributions (Wilson et al., 2012). Once relative rates of deamidation in selected peptides within a given sample are calculated, the third step uses a mixed effects model to combine the individual deamidation estimates and to obtain an overall estimate of the deamidation for a parchment sample (PQI).
The PQI can be used effectively for assessing parchment quality, as the authors show for the dataset from Orval Abbey. However, PQI could also have wider applications to the study of processed collagen, which is widely used in the food and pharmaceutical industries. In general, the study by Nair et al. is a welcome addition to a growing body of research on protein diagenesis, which will ultimately improve models for the assessment of the authenticity of biomolecular data in archaeology.
Chowdhury, P.M., Wogelius, R., Manning, P.L., Metz, L., Slimak, L., and Buckley, M. 2019. Collagen deamidation in archaeological bone as an assessment for relative decay rates. Archaeometry 61:1382–1398. https://doi.org/10.1111/arcm.12492
Fiddyment, S., Goodison, N.J., Brenner, E., Signorello, S., Price, K., and Collins, M.J.. 2021. Girding the loins? Direct evidence of the use of a medieval parchment birthing girdle from biomolecular analysis. bioRxiv. https://doi.org/10.1098/rsos.202055
Fiddyment,S., Holsinger, B., Ruzzier, C., Devine, A., Binois, A., Albarella, U., Fischer, R., Nichols, E., Curtis, A., Cheese, E., Teasdale, M.D., Checkley-Scott, C., Milner, S.J., Rudy, K.M., Johnson, E.J., Vnouček, J., Garrison, M., McGrory, S., Bradley, D.G., and Collins, M.J. 2015. Animal origin of 13th-century uterine vellum revealed using noninvasive peptide fingerprinting. Proc Natl Acad Sci U S A 112:15066–15071. https://doi.org/10.1073/pnas.1512264112
Fiddyment, S., Teasdale, M.D., Vnouček, J., Lévêque, É., Binois, A., and Collins, M.J. 2019. So you want to do biocodicology? A field guide to the biological analysis of parchment. Heritage Science 7:35. https://doi.org/10.1186/s40494-019-0278-6
Nair, B., Rodríguez Palomo, I., Markussen, B., Wiuf, C., Fiddyment, S., and Collins, M. Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data. BiorRxiv, 2022.03.13.483627, ver. 6 peer-reviewed and recommended by Peer community in Archaeology. https://doi.org/10.1101/2022.03.13.483627
Ramsøe, A., Crispin, M., Mackie, M., McGrath, K., Fischer, R., Demarchi, B., Collins, M.J., Hendy, J., and Speller, C. 2021. Assessing the degradation of ancient milk proteins through site-specific deamidation patterns. Sci Rep 11:7795. https://doi.org/10.1038/s41598-021-87125-x
Ramsøe, A., van Heekeren, V., Ponce, P., Fischer, R., Barnes, I., Speller, C., and Collins, M.J. 2020. DeamiDATE 1.0: Site-specific deamidation as a tool to assess authenticity of members of ancient proteomes. J Archaeol Sci 115:105080. https://doi.org/10.1016/j.jas.2020.105080
Schroeter, E.R., and Cleland, T.P. 2016. Glutamine deamidation: an indicator of antiquity, or preservational quality? Rapid Commun Mass Spectrom 30:251–255. https://doi.org/10.1002/rcm.7445
Simpson, J.P., Penkman, K.E.H., and Demarchi, B. 2016. The effects of demineralisation and sampling point variability on the measurement of glutamine deamidation in type I collagen extracted from bone. J Archaeol Sci 69: 29-38. https://doi.org/10.1016/j.jas.2016.02.002
Solazzo, C., Wilson, J., Dyer, J.M., Clerens, S., Plowman, J.E., von Holstein, I., Walton Rogers, P., Peacock, E.E., and Collins, M.J. 2014. Modeling deamidation in sheep α-keratin peptides and application to archeological wool textiles. Anal Chem 86:567–575. https://doi.org/10.1021/ac4026362
Teasdale, M.D., Fiddyment, S., Vnouček, J., Mattiangeli, V., Speller, C., Binois, A., Carver, M., Dand, C., Newfield, T.P., Webb, C.C., Bradley, D.G., and Collins M.J. 2017. The York Gospels: a 1000-year biological palimpsest. R Soc Open Sci 4:170988. https://doi.org/10.1098/rsos.170988
Welker, F., Soressi, M.A., Roussel, M., van Riemsdijk, I., Hublin, J.-J., and Collins, M.J. 2016. Variations in glutamine deamidation for a Châtelperronian bone assemblage as measured by peptide mass fingerprinting of collagen. STAR: Science & Technology of Archaeological Research 3:15–27. https://doi.org/10.1080/20548923.2016.1258825
Wilson, J., van Doorn, N.L., and Collins, M.J. 2012. Assessing the extent of bone degradation using glutamine deamidation in collagen. Anal Chem 84:9041–9048. https://doi.org/10.1021/ac301333t
|Parchment Glutamine Index (PQI): A novel method to estimate glutamine deamidation levels in parchment collagen obtained from low-quality MALDI-TOF data||Bharath Nair, Ismael Rodríguez Palomo, Bo Markussen, Carsten Wiuf, Sarah Fiddyment and Matthew Collins||<p style="text-align: justify;">Parchment was used as a writing material in the Middle Ages and was made using animal skins by liming them with Ca(OH)<span class="math-tex">\( _2 \)</span>. During liming, collagen peptides containing Glutamine (Q)...||Bioarchaeology, Europe, Medieval, Zooarchaeology||Beatrice Demarchi||2022-03-22 12:54:10||View|
03 Nov 2023
Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch populationBartholdy, Bjørn Peare; Hasselstrøm, Jørgen B.; Sørensen, Lambert K.; Casna, Maia; Hoogland, Menno; Historisch Genootschap Beemster; Henry, Amanda G. https://doi.org/10.5281/zenodo.7649150
Detection of plant-derived compounds in XIXth c. Dutch dental calculusRecommended by Louise Le Meillour based on reviews by Mario Zimmerman and 2 anonymous reviewers
The advent of biomolecular methods has certainly increased our overall comprehension of archaeological societies. One of the materials of choice to perform ancient DNA or proteomics analyses is dental calculus[1,2], a mineralised biofilm formed during the life of one individual. Research conducted in the past few decades has demonstrated the potential of dental calculus to retrieve information about past societies health[3–6], diet[7–11], and more recently, as a putative proxy for isotopic analyses.
Bartholdy et al. utilised the developed LC-MS/MS method to 41 buried individuals, most of them bearing pipe notches on their teeth, from the cemetery of the 19th rural settlement of Middenbeemster, the Netherlands. Along with dental calculus sampling and analysis, they undertook the skeletal and dental examination of all of the specimens in order to assess sex, age-at-death, and pathology on the two tissues. The results obtained on the dental calculus of the sampled individuals show probable consumption of tea, coffee and tobacco indicated by the detection of the various plant compounds and associated metabolites (caffeine, nicotine and salicylic acid, amongst others).
The authors were able to place their results in perspective and propose several interpretations concerning the ingestion of plant-derived products, their survival in dental calculus and the importance of their findings for our overall comprehension of health and habits of the XIXth c. Dutch population. The paper is well-written and accessible to a non-specialist audience, maximising the impact of their study. I personally really enjoyed handling this manuscript that is not only a good piece of scientific literature but also a pleasant read, the reason why I warmly recommend this paper to be accessible through PCI Archaeology.
1. Fagernäs, Z. and Warinner, C. (2023) Dental Calculus. in Handbook of Archaeological Sciences 575–590. https://doi.org/10.1002/9781119592112.ch28
2. Wright, S. L., Dobney, K. & Weyrich, L. S. (2021) Advancing and refining archaeological dental calculus research using multiomic frameworks. STAR: Science & Technology of Archaeological Research 7, 13–30. https://doi.org/10.1080/20548923.2021.1882122
3. Fotakis, A. K. et al. (2020) Multi-omic detection of Mycobacterium leprae in archaeological human dental calculus. Philos. Trans. R. Soc. Lond. B Biol. Sci. 375, 20190584. https://doi.org/10.1098/rstb.2019.0584
4. Warinner, C. et al. (2014) Pathogens and host immunity in the ancient human oral cavity. Nat. Genet. 46, 336–344. https://doi.org/10.1038/ng.2906
5. Weyrich, L. S. et al. (2017) Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus. Nature 544, 357–361. https://doi.org/10.1038/nature21674
6. Jersie-Christensen, R. R. et al. (2018) Quantitative metaproteomics of medieval dental calculus reveals individual oral health status. Nat. Commun. 9, 4744. https://doi.org/10.1038/s41467-018-07148-3
7. Hendy, J. et al. (2018) Proteomic evidence of dietary sources in ancient dental calculus. Proc. Biol. Sci. 285. https://doi.org/10.1098/rspb.2018.0977
8. Wilkin, S. et al. (2020) Dairy pastoralism sustained eastern Eurasian steppe populations for 5,000 years. Nat Ecol Evol 4, 346–355. https://doi.org/10.1038/s41559-020-1120-y
9. Bleasdale, M. et al. (2021) Ancient proteins provide evidence of dairy consumption in eastern Africa. Nat. Commun. 12, 632. https://doi.org/10.1038/s41467-020-20682-3
10. Warinner, C. et al. (2014) Direct evidence of milk consumption from ancient human dental calculus. Sci. Rep. 4, 7104. https://doi.org/10.1038/srep07104
11. Buckley, S., Usai, D., Jakob, T., Radini, A. and Hardy, K. (2014) Dental Calculus Reveals Unique Insights into Food Items, Cooking and Plant Processing in Prehistoric Central Sudan. PLoS One 9, e100808. https://doi.org/10.1371/journal.pone.0100808
12. Salazar-García, D. C., Warinner, C., Eerkens, J. W. and Henry, A. G. (2023) The Potential of Dental Calculus as a Novel Source of Biological Isotopic Data. in Exploring Human Behavior Through Isotope Analysis: Applications in Archaeological Research (eds. Beasley, M. M. & Somerville, A. D.) 125–152. https://doi.org/10.1007/978-3-031-32268-6_6
13. Sørensen, L. K., Hasselstrøm, J. B., Larsen, L. S. and Bindslev, D. A. (2021) Entrapment of drugs in dental calculus - Detection validation based on test results from post-mortem investigations. Forensic Sci. Int. 319, 110647. https://doi.org/10.1016/j.forsciint.2020.110647
14. Bartholdy, Bjørn Peare, Hasselstrøm, Jørgen B., Sørensen, Lambert K., Casna, Maia, Hoogland, Menno, Historisch Genootschap Beemster and Henry, Amanda G. (2023) Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population, Zenodo, 7649150, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7649150
|Multiproxy analysis exploring patterns of diet and disease in dental calculus and skeletal remains from a 19th century Dutch population||Bartholdy, Bjørn Peare; Hasselstrøm, Jørgen B.; Sørensen, Lambert K.; Casna, Maia; Hoogland, Menno; Historisch Genootschap Beemster; Henry, Amanda G.||<p>Dental calculus is an excellent source of information on the dietary patterns of past populations, including consumption of plant-based items. The detection of plant-derived residues such as alkaloids and their metabolites in dental calculus pr...||Bioarchaeology, Post-medieval||Louise Le Meillour||Mario Zimmerman, Anonymous||2023-07-31 17:21:40||View|
02 May 2023
Transmission of lithic and ceramic technical know-how in the Early Neolithic of central-western Europe: Shedding Light on the Social Mechanisms underlying Cultural TransitionSolène Denis, Louise Gomart, Laurence Burnez-Lanotte, Pierre Allard https://osf.io/gqnht/
A Thought Provoking Consideration of Craft in the NeolithicRecommended by Clare Burke based on reviews by Bogdana Milić and 1 anonymous reviewer
The pioneering work of Leroi-Gourhan introduced archaeologists to the concept of the chaîne opératoire, whereby, like his supervisor Mauss, Leroi-Gourhan proposed direct links between bodily actions and aspects of cultural identity. The chaîne opératoire offers a powerful conceptual tool with which to reconstruct and describe the technological practices undertaken by craftspeople, linking material objects to the cultural context in which crafts are learnt. Although initially applied to lithics, the concept today is well known in ceramic studies, as well as, other material crafts, in order to identify aspects of tradition and identity through ideas linked to technological style[3,4] and communities of practice.
Utilizing this approach, Denis et al. use the chaîne opératoire to look at both lithics and ceramics together from a diachronic viewpoint, to examine technical systems present over the transition between Linearbandkeramic (LBK) and post LBK Blicquy/Villeneuve-Saint German (BQY/VSG) timeframes. This much needed comparative and diachronic perspective, focuses on material from the sites of Vaux-et-Borset and Verlaine in Belgium, and has enabled the authors to consider the impact of changing social dynamics on these two crafts simultaneously.
The authors examine the ceramic and lithic assemblages from a macroscopic and morphological perspective in order to identify techniques of production. The data gathered testifies to the dominance of one production technique for each craft within the LBK. There is particularly striking homogeneity noted for the lithics that suggests the transmission of a single tradition over the Hesbaye area, whilst the ceramics display greater regional diversity. The picture alters somewhat for the BQY/VSG material where it seems there is an increase in the diversity of production techniques, with both the introduction of new techniques, as well as a degree of hybridization of earlier techniques to form new BQY/VSG chaînes opératoires that have LBK roots. The BQY/VSG diversity noted for the lithics is especially interesting, with the introduction of techniques that attest to increased expertise which the authors attest to the migration of an external group.
The results of this work have allowed Denis et al. to discuss multiple influences on the technical systems they identify. Rather than trying to fit the data within a single model, the authors demonstrate the need for nuance, considering the social changes associated with Neolithic migration and interactions, as multifaced and dynamic. As such, they are able to show not only the influence of contact with other groups, but that the apparent migration of external groups does not simply lead to the replacement of the crafting heritage already established at the sites they have examined.
In concluding the authors acknowledge, that as scholars push the existing state of knowledge (in this respect analysis of raw materials would make an especially important contribution), the picture presented in the paper may alter. Future work will hopefully fill in current gaps, particularly in terms of how far the trends identified extend, and the extent to which the lithic and ceramic pictures diversify on a broader geographical scale. It is certain that based on such results, future work should adopt the comparative approach presented by the authors, who have demonstrated its explanatory potential for understanding the technical and cultural groups we all study.
 Mauss, M. 2009 . Techniques, Technology and Civilisation. Edited and introduced by N. Schlanger. New York/Oxford: Durkheim Press/Berghahn Books.
 Lechtman, H. 1977. Style in Technology: some early thoughts. In H. Lechtman and R.S. Merrill (eds.) Material Culture: styles, organization and dynamics of technology. Proceedings of the American Ethnological Society 1975, St. Paul, 3-20.
 Gosselain, O. 1992. Technology and Style: Potters and Pottery Among Bafia of Cameroon. Man 27(3) 559- 586. htpps://doi.org/10.2307/2803929.
 Wenger, E. 1998. Communities of practice: Learning, meaning, and identity. Cambridge: Cambridge University Press.
 Denis, S., Gomart, L., Burnez-Lanotte, L. and Allard, P. (2023). Transmission of lithic and ceramic technical know-how in the Early Neolithic of central-western Europe: Shedding Light on the Social Mechanisms underlying Cultural Transition. OSF Preprints, gqnht, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.31219/osf.io/gqnht
|Transmission of lithic and ceramic technical know-how in the Early Neolithic of central-western Europe: Shedding Light on the Social Mechanisms underlying Cultural Transition||Solène Denis, Louise Gomart, Laurence Burnez-Lanotte, Pierre Allard||<p>Research on the European Neolithisation agrees that a process of colonisation throughout the sixth millennium BC underlies the spread of agricultural ways of life on the continent. From central to central-western Europe, this colonisation path ...||Ceramics, Europe, Lithic technology, Neolithic||Clare Burke||2022-11-18 12:03:55||View|
21 Nov 2022
Removing Barriers to Reproducible Research in ArchaeologyEmma Karoune and Esther Plomp https://doi.org/10.5281/zenodo.7320029
Three levels of reproducible workflow remove barriers for archaeologists and increase accessibilityRecommended by Ben Marwick based on reviews by Sam Leggett, Cyler Conrad, Cheng Liu and Lisa Lodwick
Over the last decade, a small but growing community of archaeologists, from a diversity of intellectual and demographic backgrounds, have been striving for computational reproducibility in their published research. In their survey of the accomplishments of this thriving community, Emma Karoune and Esther Plomp (2022) analyzed the wide variety of approaches researchers have taken to enhance the reproducibility of their research. A key contribution of this paper is their excellent synthesis of diverse approaches into three levels of increasing complexity. This is helpful because it provides multiple entry points for researchers new to the challenge of fortifying their research. Many researchers assume that computational reproducibility is only achievable if they have a high degree of technical skill with computers, or is only necessary if their work is very computationally intensive. Karoune and Plomp give three compelling reasons why reproducibility is important for all archaeological research, and through their three levels they demonstrate that how these levels can be accomplished with basic, non-specialized computer skills and widely used free software. They showcase exemplary work from a variety of archaeologists to show how practical and achievable reproducible research is for all archaeologists. They advocate for archaeologists to use the most widely used and supported tools and services to support their reproducible research, such as the R and Python programming languages for data analysis, and Git and GitHub for collaboration.
This paper, with its extensive appendix including thoughtful responses to frequently asked questions about reproducible research in archaeology, is likely to have a wide reach and influence, beyond previous works on this topic that have largely focused on technical details. Karoune and Plomp have provided the on-ramp for a generation of archaeologists who will find their questions about reproducible research answered here. They will also find an agreeable entry point to reproducible research in one of the three levels described by the authors. Will every archaeologist embrace this way of working? Should they? The work of Leonelli (2018) can help us anticipate the answers to these questions. Leonelli asks where are the limits to reproducibility, and how do the characteristics of different ways of knowing affect the desirability of reproducibility? Leonelli's work invites us to consider that there will be archaeologists coming from different epistemic cultures for whom the motivations presented by Karoune and Plomp will not resonate. For example, archaeologists engaged in mostly hermeneutical social science and humanities research, who do little or no quantitative analysis and statistics, are unlikely to see reproducibility as meaningful or desirable for their work. We can describe these researchers as working in interpretative or constructivist epistemic cultures. In these cultures, the particulars of how an individual researcher engages with their subject are exclusive and unique, and they would argue it cannot be fully captured or shared in an meaningful way (Elman and Kapiszewski 2017). Here, knowledge is situational, emerging from a specific, once-off combination of people and circumstances. One example in archaeology is the chaîne opératoire approach of stone artefact analysis, which Monnier and Missal (2014:61) describe as "based upon the analyst's experience and intuition, and it is not replicable, nor quantifiable". To make sense of this example we can draw on Galison's (1997) concept of 'image traditions' and 'logic traditions'. An image tradition is a way of knowing that is qualitative, based on composing narratives from drawings and photographs. A logic tradition is based on the use of instruments and statistical methods to collect standardised quantitative data. Chaîne opératoire approaches fall into the image tradition, along with many other ways of working in archaeology that do not generate numbers or use them to support claims about the past. Archaeologists working in a logic tradition will find reproducible research to be more meaningful than those working in an image tradition.
We should be mindful not to claim that one epistemic culture is superior to another because reproducibility is not meaningful or attainable for researchers in one culture. Such a claim would threaten the plurality that is essential for the reliability of scientific knowledge (Massimi 2022). Instead we should identify those communities in archaeology where reproducible research is both meaningful and attainable, but has not yet been widely embraced. That is the where the most beneficial effects can be expected. According to Leonelli's (2018) framework, we can recognise these communities by a few basic characteristics. For example: they are doing computationally intensive archaeology, such as using or writing software to collect, simulate, analyse or visualise data; they are doing experimental archaeology; or they are making knowledge claims that are supported by tables of numeric data and data visualisations. Archaeologists whose work shares one or more of these characteristics will find the guidance provided here by Karoune and Plomp to be highly instructive and relevant, and stand the most to benefit from it.
But it is not only individual archaeological scientists that have potential to benefit from how Karoune and Plomp have lowered the barriers to reproducible research. An especially important implication of this paper is that by lowering the barriers to reproducible research, Karoune and Plomp help us all to lower barriers to participation in archaeology in general. Documenting our research transparently, and sharing our materials (such as data and code and so on) openly, can profoundly change how others can participate in archaeology. By doing this, we are enabling students and researchers elsewhere, for example in low and middle income locations, to use our materials in their teaching and learning. Other researchers and students can apply our methods to their data, and combine their data with ours to achieve syntheses beyond what a single project can do. Similarly, for archaeologists working with local, descendant or marginalized communities, the tools of reproducible research are vital for enabling community members to have full access to the archaeological process, and thus reproducibility may be considered a necessity for decolonising the discipline. Karoune and Plomp present the CARE principles (Carroll et al. 2020) to guide archaeologists in ensuring community control of data so that reproducibility can be ethically accomplished with community safety and well-being as a priority. This may have a profoundly positive impact on the demographics of archaeology, as it lowers the barriers of meaningful participation by people far beyond our immediate groups of collaborators.
Making archaeology more accessible is of critical importance in stemming the negative social impacts of pseudoarchaeologists, who often claim that archaeologists actively suppress the truth of the archaeological record through secrecy, elitism, and exclusiveness. The harm in this is twofold. First, that pseudoarchaeology typically erases Indigenous heritage by claiming that their past achievements were due to an ancient, extinct advanced civilization, not Indigenous people. These claims are often adopted by white supremacists to support racist and antisemitic conspiracy theories (Turner and Turner 2021), which sometimes leads to prejudice, physical violence, radicalization and extremism. A second type of harm that can come from claims of secrecy and elitism is it drains public trust in experts, leading to science denial. Not only trust in archaeologists, but trust in many kinds of experts, including those working on urgent contemporary issues such as public health and climate change. Karoune and Plomp's work is important here because it provides a practical and affordable pathway for archaeologists to fight claims of secrecy and elitism by sharing their work in ways that make it possible for non-academics to inspect the analyses and logic in detail. Claims of secrecy and elitism can be easily countered by openness, transparently and reproducibility by archaeologists. This is not only useful for tackling pseudoarchaeologists, but also in enacting an ethic of care, framing members of the public as people that not only care about archaeology as part of humanity's shared heritage, but also care for the construction of reliable interpretations of the archaeological record to provide secure and authentic foundations for their social identities and relationships (Wylie et al 2018; de la Bellacasa 2011). By striving for reproducible research in the way described by Karoune and Plomp, we are practicing a kind of reciprocal care among ourselves as archaeologists, and between archaeologists and members of the public as two communities who care about the human past.
Karoune, E., and Plomp, E. (2022). Removing Barriers to Reproducible Research in Archaeology. Zenodo, 7320029, ver. 5 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7320029
de la Bellacasa, M. P. (2011). Matters of care in technoscience: Assembling neglected things. Social Studies of Science, 41(1), 85–106. https://doi.org/10.1177/0306312710380301
Carroll, S. R., Garba, I., Figueroa-Rodríguez, O. L., Holbrook, J., Lovett, R., Materechera, S., Parsons, M., Raseroka, K., Rodriguez-Lonebear, D., Rowe, R., Sara, R., Walker, J. D., Anderson, J., and Hudson, M. (2020). The CARE Principles for Indigenous Data Governance. Data Science Journal, 19(1), Article 1. https://doi.org/10.5334/dsj-2020-043
Elman, C., and Kapiszewski, D. (2017). Benefits and Challenges of Making Qualitative Research More Transparent. Inside Higher Ed 2017, http://web.archive.org/web/20220407064134/https://www.insidehighered.com/blogs/rethinking-research/benefits-and-challenges-making-qualitative-research-more-transparent (accessed 21 Oct, 2022).
Galison, P. (1997). Image and logic: a material culture of microphysics. Chicago (IL): University of Chicago Press.
Leonelli, S. (2018). Re-Thinking Reproducibility as a Criterion for Research Quality [preprint]. Available online: http://philsci-archive.pitt.edu/id/eprint/14352 (Accessed 21 Oct 2022).
Massimi, M. (2022). Perspectival realism. Oxford University Press.
Monnier, G. F., and Kele M.. "Another Mousterian debate? Bordian facies, chaîne opératoire technocomplexes, and patterns of lithic variability in the western European Middle and Upper Pleistocene." Quaternary International 350 (2014): 59-83. https://doi.org/10.1016/j.quaint.2014.06.053
Turner, D. D., and Turner, M. I. (2021). “I’m Not Saying It Was Aliens”: An Archaeological and Philosophical Analysis of a Conspiracy Theory. In A. Killin and S. Allen-Hermanson (Eds.), Explorations in Archaeology and Philosophy (pp. 7–24). Springer International Publishing. https://doi.org/10.1007/978-3-030-61052-4_2
Wylie, C., Neeley, K., and Ferguson, S. (2018). Beyond Technological Literacy: Open Data as Active Democratic Engagement? Digital Culture & Society, 4(2), 157–182. https://doi.org/10.14361/dcs-2018-0209
|Removing Barriers to Reproducible Research in Archaeology||Emma Karoune and Esther Plomp||<p>Reproducible research is being implemented at different speeds in different disciplines, and Archaeology is at the start of this journey. Reproducibility is the practice of reanalysing data by taking the same steps and producing the same or sim...||Computational archaeology||Ben Marwick||2022-06-07 10:02:46||View|
02 Sep 2023
Research workflows, paradata, and information visualisation: feedback on an exploratory integration of issues and practices - MEMORIA ISDudek Iwona, Blaise Jean-Yves https://doi.org/10.5281/zenodo.8311129
Using information visualisation to improve traceability, transmissibility and verifiability in research workflowsRecommended by Isto Huvila based on reviews by Adéla Sobotkova and 2 anonymous reviewers
The paper “Research workflows, paradata, and information visualisation: feedback on an exploratory integration of issues and practices - MEMORIA IS” (Dudek & Blaise, 2023) describes a prototype of an information system developed to improve the traceability, transmissibility and verifiability of archaeological research workflows. A key aspect of the work with MEMORIA is to make research documentation and the workflows underpinning the conducted research more approachable and understandable using a series of visual interfaces that allow users of the system to explore archaeological documentation, including metadata describing the data and paradata that describes its underlying processes. The work of Dudek and Blaise address one of the central barriers to reproducibility and transparency of research data and propose a set of both theoretically and practically well-founded tools and methods to solve this major problem. From the reported work on MEMORIA IS, information visualisation and the proposed tools emerge as an interesting and potentially powerful approach for a major push in improving the traceability, transmissibility and verifiability of research data through making research workflows easier to approach and understand.
In comparison to technical work relating to archaeological data management, this paper starts commendably with a careful explication of the conceptual and epistemic underpinnings of the MEMORIA IS both in documentation research, knowledge organisation and information visualisation literature. Rather than being developed on the basis of a set of opaque assumptions, the meticulous description of the MEMORIA IS and its theoretical and technical premises is exemplary in its transparence and richness and has potential for a long-term impact as a part of the body of literature relating to the development of archaeological documentation and documentation tools. While the text is sometimes fairly densely written, it is worth taking the effort to read it through. Another major strength of the paper is that it provides a rich set of examples of the workings of the prototype system that makes it possible to develop a comprehensive understanding of the proposed approaches and assess their validity.
As a whole, this paper and the reported work on MEMORIA IS forms a worthy addition to the literature on and practical work for developing critical infrastructures for data documentation, management and access in archaeology. Beyond archaeology and the specific context of the discussed work discussed this paper has obvious relevance to comparable work in other fields.
Dudek, I. and Blaise, J.-Y. (2023) Research workflows, paradata, and information visualisation: feedback on an exploratory integration of issues and practices - MEMORIA IS, Zenodo, 8252923, ver. 3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.8252923
|Research workflows, paradata, and information visualisation: feedback on an exploratory integration of issues and practices - MEMORIA IS||Dudek Iwona, Blaise Jean-Yves||<p>The paper presents an exploratory web information system developed as a reaction to practical and epistemological questions, in the context of a scientific unit studying the architectural heritage (from both historical sciences perspective, and...||Computational archaeology||Isto Huvila||2023-05-02 12:50:39||View|
23 Nov 2023
Percolation Package - From script sharing to package publicationSophie C Schmidt; Simon Maddison https://doi.org/10.5281/zenodo.7966497
Sharing Research Code in ArchaeologyRecommended by James Allison based on reviews by Thomas Rose, Joe Roe and 1 anonymous reviewer
The paper “Percolation Package – From Script Sharing to Package Publication” by Sophie C. Schmidt and Simon Maddison (2023) describes the development of an R package designed to apply Percolation Analysis to archaeological spatial data. In an earlier publication, Maddison and Schmidt (2020) describe Percolation Analysis and provide case studies that demonstrate its usefulness at different spatial scales. In the current paper, the authors use their experience collaborating to develop the R package as part of a broader argument for the importance of code sharing to the research process.
The paper begins by describing the development process of the R package, beginning with borrowing code from a geographer, refining it to fit archaeological case studies, and then collaborating to further refine and systematize the code into an R package that is more easily reusable by other researchers. As the review by Joe Roe noted, a strength of the paper is “presenting the development process as it actually happens rather than in an idealized form.” The authors also include a section about the lessons learned from their experience.
Moving on from the anecdotal data of their own experience, the authors also explore code sharing practices in archaeology by briefly examining two datasets. One dataset comes from “open-archaeo” (https://open-archaeo.info/), an on-line list of open-source archaeological software maintained by Zack Batist. The other dataset includes articles published between 2018 and 2023 in the Journal of Computer Applications in Archaeology. Schmidt and Maddison find that these two datasets provide contrasting views of code sharing in archaeology: many of the resources in the open-archaeo list are housed on Github, lack persistent object identifiers, and many are not easily findable (other than through the open-archaeo list). Research software attached to the published articles, on the other hand, is more easily findable either as a supplement to the published article, or in a repository with a DOI.
The examination of code sharing in archaeology through these two datasets is preliminary and incomplete, but it does show that further research into archaeologists’ code-writing and code-sharing practices could be useful. Archaeologists often create software tools to facilitate their research, but how often? How often is research software shared with published articles? How much attention is given to documentation or making the software usable for other researchers? What are best (or good) practices for sharing code to make it findable and usable? Schmidt and Maddison’s paper provides partial answers to these questions, but a more thorough study of code sharing in archaeology would be useful. Differences among journals in how often they publish articles with shared code, or the effects of age, gender, nationality, or context of employment on attitudes toward code sharing seem like obvious factors for a future study to consider.
Shared code that is easy to find and easy to use benefits the researchers who adopt code written by others, but code authors also have much to gain by sharing. Properly shared code becomes a citable research product, and the act of code sharing can lead to productive research collaborations, as Schmidt and Maddison describe from their own experience. The strength of this paper is the attention it brings to current code-sharing practices in archaeology. I hope the paper will also help improve code sharing in archaeology by inspiring more archaeologists to share their research code so other researchers can find and use (and cite) it.
Maddison, M.S. and Schmidt, S.C. (2020). Percolation Analysis – Archaeological Applications at Widely Different Spatial Scales. Journal of Computer Applications in Archaeology, 3(1), p.269–287. https://doi.org/10.5334/jcaa.54
Schmidt, S. C., and Maddison, M. S. (2023). Percolation Package - From script sharing to package publication, Zenodo, 7966497, ver. 3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7966497
|Percolation Package - From script sharing to package publication||Sophie C Schmidt; Simon Maddison||<p>In this paper we trace the development of an R-package starting with the adaptation of code from a different field, via scripts shared between colleagues, to a published package that is being successfully used by researchers world-wide. Our aim...||Computational archaeology||James Allison||2023-05-24 15:40:15||View|
06 Aug 2023
A Focus on the Future of our Tiny Piece of the Past: Digital Archiving of a Long-term Multi-participant Regional ProjectScott Madry, Gregory Jansen, Seth Murray, Elizabeth Jones, Lia Willcoxon, Ebtihal Alhashem https://doi.org/10.5281/zenodo.7967035
A meticulous description of archiving research data from a long-running landscape research projectRecommended by Isto Huvila based on reviews by Dominik Hagmann and Iwona Dudek
The paper “A Focus on the Future of our Tiny Piece of the Past: Digital Archiving of a Long-term Multi-participant Regional Project” (Madry et al., 2023) describes practices, challenges and opportunities encountered in digital archiving of a landscape research project running in Burgundy, France for more than 45 years. As an unusually long-running multi-disciplinary undertaking working with a large variety of multi-modal digital and non-digital data, the Burgundy project has lived through the development of documentation and archiving technologies from the 1970s until today and faced many of the challenges relating to data management, preservation and migration.
The major strenght of the paper is that it provides a detailed description of the evolution of digital data archiving practices in the project including considerations about why some approaches were tested and abandoned. This differs from much of the earlier literature where it has been more common to describe individual solutions how digital archiving was either planned or was performed at one point of time. A longitudinal description of what was planned, how and why it has worked or failed so far, as described in the paper, provides important insights in the everyday hurdles and ways forward in digital archiving. As a description of a digital archiving initiative, the paper makes a valuable contribution for the data archiving scholarship as a case description of practices and considerations in one research project. For anyone working with data management in a research project either as a researcher or data manager, the text provides useful advice on important practical matters to consider ahead, during and after the project. The main advice the authors are giving, is to plan and act for data preservation from the beginning of the project rather than doing it afterwards. To succeed in this, it is crucial to be knowledgeable of the key concepts of data management—such as “digital data fixity, redundant backups, paradata, metadata, and appropriate keywords” as the authors underline—including their rationale and practical implications. The paper shows also that when and if unexpected issues raise, it is important to be open for different alternatives, explore ways forward, and in general be flexible.
The paper makes also a timely contribution to the discussion started at the session “Archiving information on archaeological practices and work in the digital environment: workflows, paradata and beyond” at the Computer Applications and Quantitative 2023 conference in Amsterdam where it was first presented. It underlines the importance of understanding and communicating the premises and practices of how data was collected (and made) and used in research for successful digital archiving, and the similar pertinence of documenting digital archiving processes to secure the keeping, preservation and effective reuse of digital archives possible.
Madry, S., Jansen, G., Murray, S., Jones, E., Willcoxon, L. and Alhashem, E. (2023) A Focus on the Future of our Tiny Piece of the Past: Digital Archiving of a Long-term Multi-participant Regional Project, Zenodo, 7967035, ver. 3 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7967035
|A Focus on the Future of our Tiny Piece of the Past: Digital Archiving of a Long-term Multi-participant Regional Project||Scott Madry, Gregory Jansen, Seth Murray, Elizabeth Jones, Lia Willcoxon, Ebtihal Alhashem||<p>This paper will consider the practical realities that have been encountered while seeking to create a usable Digital Archiving system of a long-term and multi-participant research project. The lead author has been involved in archaeologic...||Computational archaeology, Environmental archaeology, Landscape archaeology||Isto Huvila||2023-05-24 18:46:34||View|
01 Dec 2022
Surface texture analysis in Toothfrax and MountainsMap® SSFA module: Different software packages, different results?Ivan CALANDRA, Konstantin BOB, Gildas MERCERON, François BLATEYRON, Andreas HILDEBRANDT, Ellen SCHULZ-KORNAS, Antoine SOURON, Daniela E. WINKLER https://doi.org/10.5281/zenodo.4671438
An important comparison of software for Scale Sensitive Fractal Analysis : are ancient and new results compatible?Recommended by Alain Queffelec and Florent Rivals based on reviews by Antony Borel and 2 anonymous reviewers
The community of archaeologists, bioanthropologist and paleontologists relying on tools use-wear and dental microwear has grown in the recent years, mainly driven by the spread of confocal microscopes in the laboratories. If the diversity of microscopes is quite high, the main software used for 3D surface texture data analysis are mostly different versions of the same Mountains Map core. In addition to this software, since the beginning of 3D surface texture analysis in dental microwear, surface sensitive fractal analysis (SSFA) initially developed for industrial research (Brown & Savary, 1991) have been performed in our disciplines with the Sfrax/Toothfrax software for two decades (Ungar et al., 2003). This software being discontinued, these calculations have been integrated to the new versions of Mountains Map, with multi-core computing, full integration in the software and an update of the calculation itself.
New research based on these standard parameters of surface texture analysis will be, from now on, mainly calculated with this new add-on of Mountains Map, and will be directly compared with the important literature based on the previous software. The question addressed by Calandra et al. (2022), gathering several prominent researchers in this domain including the Mountains Map developer F. Blateyron, is key for the future research: can we directly compare SSFA results from both software?
Thanks to a Bayesian approach to this question, and comparing results calculated with both software on three different datasets (two on dental microwear, one on lithic raw materials), the authors show that the two software gives statistically different results for all surface texture parameters tested in the paper. Nevertheless, applying the new calculation to the datasets, they also show that the results published in original studies with these datasets would have been similar. Authors also claim that in the future, researchers will need to re-calculate the fractal parameters of previously published 3D surfaces and cannot simply integrate ancient and new data together.
We also want to emphasize the openness of the work published here. All datasets have been published online and will be probably very useful for future methodological works. Authors also published their code for statistical comparison of datasets, and proposed a fully reproducible article that allowed the reviewers to check the content of the paper, which can also make this article of high interest for student training.
This article is therefore a very important methodological work for the community, as noted by all three reviewers. It will certainly support the current transition between the two software packages and it is necessary that all surface texture specialists take these results and the recommendation of authors into account: calculate again data from ancient measurements, and share the 3D surface measurements on open access repositories to secure their access in the future.
Brown CA, and Savary G (1991) Describing ground surface texture using contact profilometry and fractal analysis. Wear, 141, 211–226. https://doi.org/10.1016/0043-1648(91)90269-Z
Calandra I, Bob K, Merceron G, Blateyron F, Hildebrandt A, Schulz-Kornas E, Souron A, and Winkler DE (2022) Surface texture analysis in Toothfrax and MountainsMap® SSFA module: Different software packages, different results? Zenodo, 7219877, ver. 4 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7219877
Ungar PS, Brown CA, Bergstrom TS, and Walker A (2003) Quantification of dental microwear by tandem scanning confocal microscopy and scale-sensitive fractal analyses. Scanning: The Journal of Scanning Microscopies, 25, 185–193. https://doi.org/10.1002/sca.4950250405
|Surface texture analysis in Toothfrax and MountainsMap® SSFA module: Different software packages, different results?||Ivan CALANDRA, Konstantin BOB, Gildas MERCERON, François BLATEYRON, Andreas HILDEBRANDT, Ellen SCHULZ-KORNAS, Antoine SOURON, Daniela E. WINKLER||<p>The scale-sensitive fractal analysis (SSFA) of dental microwear textures is traditionally performed using the software Toothfrax. SSFA has been recently integrated to the software MountainsMap® as an optional module. Meanwhile, Toothfrax suppor...||Computational archaeology, Palaeontology, Traceology||Alain Queffelec||Anonymous, John Charles Willman, Antony Borel||2022-07-07 09:58:50||View|
05 Jun 2023
SEAHORS: Spatial Exploration of ArcHaeological Objects in R ShinyROYER, Aurélien, DISCAMPS, Emmanuel, PLUTNIAK, Sébastien, THOMAS, Marc https://doi.org/10.5281/zenodo.7957154
Analyzing piece-plotted artifacts just got simpler: A good solution to the wrong problem?Recommended by Reuven Yeshurun based on reviews by Frédéric Santos, Jacqueline Meier and Maayan Lev
Paleolithic archaeologists habitually measure 3-coordinate data for artifacts in their excavations. This was first done manually, and in the last three decades it is usually performed by a total station and associated hardware. While the field recording procedure is quite straightforward, visualizing and analyzing the data are not, often requiring specialized proprietary software or coding expertise. Here, Royer and colleagues (2023) present the SEAHORS application, an elegant solution for the post-excavation analysis of artifact coordinate data that seems to be instantly useful for numerous archaeologists. SEAHORS allows one to import and organize field data (Cartesian coordinates and point description), which often comes in a variety of formats, and to create various density and distribution plots. It is specifically adapted to the needs of archaeologists, is free and accessible, and much simpler to use than many commercial programs. The authors further demonstrate the use of the application in the post-excavation analysis of the Cassenade Paleolithic site (see also Discamps et al., 2019).
While in no way detracting from my appreciation of Royer et al.’s (2023) work, I would like to play the devil’s advocate by asking whether, in the majority of cases, field recording of artifacts in three coordinates is warranted. Royer et al. (2023) regard piece plotting as “…indispensable to propose reliable spatial planimetrical and stratigraphical interpretations” but this assertion does not hold in all (or most) cases, where careful stratigraphic excavation employing thin volumetric units would do just as well.
Moreover, piece-plotting has some serious drawbacks. The recording often slows excavations considerably, beyond what is needed for carefully exposing and documenting the artifacts in their contexts, resulting in smaller horizontal and vertical exposures (e.g., Gilead, 2002). This typically hinders a fuller stratigraphic and contextual understanding of the excavated levels and features. Even worse, the method almost always creates a biased sample of “coordinated artifacts”, in which the most important items for understanding spatial patterns and site-formation processes – the small ones – are underrepresented. Some projects run the danger of treating the coordinated artifacts as bearing more significance than the sieve-recovered items, preferentially studying the former with no real justification. Finally, the coordinated items often go unassigned to a volumetric unit, effectively disconnecting them from other types of data found in the same depositional contexts.
The advantages of piece-plotting may, in some cases, offset the disadvantages. But what I find missing in the general discourse (certainly not in the recommended preprint) is the “theory” behind the seemingly technical act of 3-coordinate recording (Yeshurun, 2022). Being in effect a form of sampling, this practice needs a rethink about where and how to be applied; what depositional contexts justify it, and what the goals are. These questions should determine if all “visible” artifacts are plotted, or just an explicitly defined sample of them (e.g., elongated items above a certain length threshold, which should be more reliable for fabric analysis), or whether the circumstances do not actually justify it. In the latter case, researchers sometimes opt for using “virtual coordinates” within in each spatial unit (typically 0.5x0.5 m), essentially replicating the data that is generated by “real” coordinates and integrating the sieve-recovered items as well. In either case, Royer et al.’s (2023) solution for plotting and visualizing labeled points within intra-site space would indeed be an important addition to the archaeologists’ tool kits.
Discamps, E., Bachellerie, F., Baillet, M. and Sitzia, L. (2019). The use of spatial taphonomy for interpreting Pleistocene palimpsests: an interdisciplinary approach to the Châtelperronian and carnivore occupations at Cassenade (Dordogne, France). Paleoanthropology 2019, 362–388. https://doi.org/10.4207/PA.2019.ART136
Gilead, I. (2002). Too many notes? Virtual recording of artifacts provenance. In: Niccolucci, F. (Ed.). Virtual Archaeology: Proceedings of the VAST Euroconference, Arezzo 24–25 November 2000. BAR International Series 1075, Archaeopress, Oxford, pp. 41–44.
Royer, A., Discamps, E., Plutniak, S. and Thomas, M. (2023). SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny Zenodo, 7957154, ver. 2 peer-reviewed and recommended by Peer Community in Archaeology. https://doi.org/10.5281/zenodo.7929462
Yeshurun, R. (2022). Intra-site analysis of repeatedly occupied camps: Sacrificing “resolution” to get the story. In: Clark A.E., Gingerich J.A.M. (Eds.). Intrasite Spatial Analysis of Mobile and Semisedentary Peoples: Analytical Approaches to Reconstructing Occupation History. University of Utah Press, pp. 27–35.
|SEAHORS: Spatial Exploration of ArcHaeological Objects in R Shiny||ROYER, Aurélien, DISCAMPS, Emmanuel, PLUTNIAK, Sébastien, THOMAS, Marc||<p style="text-align: justify;">This paper presents SEAHORS, an R shiny application available as an R package, dedicated to the intra-site spatial analysis of piece-plotted archaeological remains. This open-source script generates 2D and 3D scatte...||Computational archaeology, Spatial analysis, Theoretical archaeology||Reuven Yeshurun||2023-02-24 16:01:44||View|
24 Jun 2021
The strength of parthood ties. Modelling spatial units and fragmented objects with the TSAR method – Topological Study of Archaeological RefittingSébastien Plutniak https://osf.io/q2e69
A practical computational approach to stratigraphic analysis using conjoinable material culture.Recommended by Hector A. Orengo based on reviews by Robert Bischoff, Matthew Peeples and 1 anonymous reviewer
The paper by Plutniak  presents a new method that uses refitting to help interpret stratigraphy using the topological distribution of conjoinable material culture. This new method opens up new avenues to the archaeological use of network analysis but also to assess the integrity of interpreted excavation layers. Beyond its evident applicability to standard excavation practice, the paper presents a series of characteristics that exemplify archaeological publication best practices and, as someone more versed in computational than in refitting studies I would like to comment upon.
It was no easy task to find adequate reviewers for this paper as it combines techniques and expertise that are not commonly found together in individual researchers. However, Plutniak, with help from three reviewers, particularly M. Peeples, a leading figure in archaeological applications of network science, makes a considerable effort to be accessible to non-specialist archaeologists. The core Topological Study of Archaeological Refitting (TSAR) method is freely accessible as the R package archeofrag, which is available at the Comprehensive R Archive Network (https://CRAN.R-project.org/package=archeofrag) that can be applied without the need to understand all its mathematical, graph theory and coding aspects. Beside these, an online interface including test data has been provided (https://analytics.huma-num.fr/Sebastien.Plutniak/archeofrag/), which aims to ease access to the method to those archaeologists inexperienced with R. Finally, supplementary material showing how to use the package and evaluating its potential through excellent examples is provided as both pdf and Rmw (Sweave) files. This is an important companion for the paper as it allows a better understanding of the methods presented in the paper and its practical application.
The author shows particular care in testing the potential and capabilities of the method. For example, a function is provided “frag.observer.failure” to test the robustness of the edge count method against the TSAR method, which is able to prove that TSAR can deal well with incomplete information. As a further step in this direction both simulated and real field-acquired data are used to test the method which further proves that archeofrag is not only able to quantitatively assess the mixture of excavated layers but to propose meaningful alternatives, which no doubt will add an increased methodological consistency and thoroughness to previous quantitative approaches to material refitting work, even when dealing with very complex stratigraphies.
All in all, this paper makes an important contribution to core archaeological practice through the use of innovative, reproducible and accessible computational methods. I fully endorse it for the conscious and solid methods it presents but also for its adherence to open publication practices. I hope that it can become of standard use in the reconstruction of excavated stratigraphical layers through conjoinable material culture.
 Plutniak, S. 2021. The Strength of Parthood Ties. Modelling Spatial Units and Fragmented Objects with the TSAR Method – Topological Study of Archaeological Refitting. OSF Preprints, q2e69, ver. 3 Peer-reviewed and recommended by PCI Archaeology. https://doi.org/10.31219/osf.io/q2e69.
|The strength of parthood ties. Modelling spatial units and fragmented objects with the TSAR method – Topological Study of Archaeological Refitting||Sébastien Plutniak||<p>Refitting and conjoinable pieces have long been used in archaeology to assess the consistency of discrete spatial units, such as layers, and to evaluate disturbance and post-depositional processes. The majority of current methods, despite their...||Computational archaeology, Taphonomy||Hector A. Orengo||2021-01-14 18:31:01||View|