diff --git a/joss.06716/10.21105.joss.06716.crossref.xml b/joss.06716/10.21105.joss.06716.crossref.xml new file mode 100644 index 0000000000..722372fa22 --- /dev/null +++ b/joss.06716/10.21105.joss.06716.crossref.xml @@ -0,0 +1,620 @@ + + + + 20240522T114024-3ef6d90c33f1629b363ab15b9261a0d27306ff3b + 20240522114024 + + JOSS Admin + admin@theoj.org + + The Open Journal + + + + + Journal of Open Source Software + JOSS + 2475-9066 + + 10.21105/joss + https://joss.theoj.org + + + + + 05 + 2024 + + + 9 + + 97 + + + + fellingdater: a toolkit to estimate, report and combine +felling dates derived from historical tree-ring series. + + + + Kristof + Haneca + https://orcid.org/0000-0002-7719-8305 + + + + 05 + 22 + 2024 + + + 6716 + + + 10.21105/joss.06716 + + + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + http://creativecommons.org/licenses/by/4.0/ + + + + Software archive + 10.5281/zenodo.11186275 + + + GitHub review issue + https://github.com/openjournals/joss-reviews/issues/6716 + + + + 10.21105/joss.06716 + https://joss.theoj.org/papers/10.21105/joss.06716 + + + https://joss.theoj.org/papers/10.21105/joss.06716.pdf + + + + + + Precise tree-ring dating of building +activities despite the absence of bark: A case-study on medieval church +roofs in damme, belgium + Haneca + Dendrochronologia + 1 + 30 + 10.1016/j.dendro.2011.06.002 + 2012 + Haneca, K., & Debonne, V. (2012). +Precise tree-ring dating of building activities despite the absence of +bark: A case-study on medieval church roofs in damme, belgium. +Dendrochronologia, 30(1), 23–34. +https://doi.org/10.1016/j.dendro.2011.06.002 + + + A slice through time. Dendrochronology and +precision dating + Baillie + 1995 + Baillie, M. G. L. (1995). A slice +through time. Dendrochronology and precision dating. B.T. Batsford +Ltd. + + + Oaks, tree-rings and wooden cultural +heritage: A review of the main characteristics and applications of oak +dendrochronology in europe + Haneca + Journal of Archaeological +Science + 1 + 36 + 10.1016/j.jas.2008.07.005 + 2009 + Haneca, K., Cufar, K., & +Beeckman, H. (2009). Oaks, tree-rings and wooden cultural heritage: A +review of the main characteristics and applications of oak +dendrochronology in europe. Journal of Archaeological Science, 36(1), +1–11. https://doi.org/10.1016/j.jas.2008.07.005 + + + Dendroarchaeology in Europe + Tegel + Frontiers in Ecology and +Evolution + 10 + 10.3389/fevo.2022.823622 + 2022 + Tegel, W., Muigg, B., Skiadaresis, +G., Vanmoerkerke, J., & Seim, A. (2022). Dendroarchaeology in +Europe. Frontiers in Ecology and Evolution, 10, 823622. +https://doi.org/10.3389/fevo.2022.823622 + + + A statistical model for the prediction of the +number of sapwood rings in Scots pine (Pinus sylvestris +L.) + Edvardsson + Dendrochronologia + 74 + 10.1016/j.dendro.2022.125963 + 2022 + Edvardsson, J., Rögnvaldsson, K., +Helgadóttir, E. D., Linderson, H., & Hrafnkelsson, B. (2022). A +statistical model for the prediction of the number of sapwood rings in +Scots pine (Pinus sylvestris L.). Dendrochronologia, 74, 125963. +https://doi.org/10.1016/j.dendro.2022.125963 + + + The Zurich method for sapwood +estimation + Bleicher + Dendrochronologia + 64 + 10.1016/j.dendro.2020.125776 + 2020 + Bleicher, N., Walder, F., Gut, U., +& Bolliger, M. (2020). The Zurich method for sapwood estimation. +Dendrochronologia, 64, 125776. +https://doi.org/10.1016/j.dendro.2020.125776 + + + Determination of the number of sapwood annual +rings in oak in the region of southern moravia + Rybnicek + Journal of Forest Science + 3 + 52 + 10.17221/4496-JFS + 2006 + Rybnicek, M., Vavrik, H., & +Hubeny, R. (2006). Determination of the number of sapwood annual rings +in oak in the region of southern moravia. Journal of Forest Science, +52(3), 141–146. +https://doi.org/10.17221/4496-JFS + + + A 700 year dating chronology for northern +france. Applications of tree-ring studies. Current research in +dendrochronology and related subjects + Pilcher + BAR International Series + 333 + 1987 + Pilcher, J. R. (1987). A 700 year +dating chronology for northern france. Applications of tree-ring +studies. Current research in dendrochronology and related subjects. BAR +International Series, 333, 127–139. + + + Jahrringchronologische datierung von +eichenhölzern ohne waldkante + Hollstein + Bonner Jahrbücher + 165 + 1965 + Hollstein, E. (1965). +Jahrringchronologische datierung von eichenhölzern ohne waldkante. +Bonner Jahrbücher, 165, 12–27. + + + Mitteleuropäische eichenchronologie: Trierer +dendrochronologische forschungen zur archäologie und +kunstgeschichte + Hollstein + 1980 + Hollstein, E. (1980). +Mitteleuropäische eichenchronologie: Trierer dendrochronologische +forschungen zur archäologie und kunstgeschichte. Verlag Phillipp von +Zabern. + + + Aufbau und anwendung der dendrochronologie +für eichenholz in polen + Wazny + 1990 + Wazny, T. (1990). Aufbau und +anwendung der dendrochronologie für eichenholz in polen [PhD +thesis]. + + + The interpretation, presentation and use of +tree-ring dates + Miles + Vernacular architecture + 28 + 10.1179/030554797786050563 + 1997 + Miles, D. (1997). The interpretation, +presentation and use of tree-ring dates. Vernacular Architecture, 28, +40–56. +https://doi.org/10.1179/030554797786050563 + + + Sapwood estimates of pedunculate oak (Quercus +robur L.) in eastern Baltic + Sohar + Dendrochronologia + 1 + 30 + 10.1016/j.dendro.2011.08.001 + 2012 + Sohar, K., Vitas, A., & +Läänelaid, A. (2012). Sapwood estimates of pedunculate oak (Quercus +robur L.) in eastern Baltic. Dendrochronologia, 30(1), 49–56. +https://doi.org/10.1016/j.dendro.2011.08.001 + + + A tree-ring chronology from the western part +of sweden. Sapwood and a dating problem + Bräthen + Second nordic conference on the application +of scientific methods in archaeology, PACT 7(1) + 1982 + Bräthen, A. (1982). A tree-ring +chronology from the western part of sweden. Sapwood and a dating +problem. In T. Hackens & V. Mejdahl (Eds.), Second nordic conference +on the application of scientific methods in archaeology, PACT 7(1) (pp. +27–35). + + + Sapwood estimates in the interpretation of +tree-ring dates + Hughes + Journal of Archaeological +Science + 8 + 10.1016/0305-4403(81)90037-6 + 1981 + Hughes, M. K., Milsom, S. J., & +Leggett, P. A. (1981). Sapwood estimates in the interpretation of +tree-ring dates. Journal of Archaeological Science, 8, 381–390. +https://doi.org/10.1016/0305-4403(81)90037-6 + + + Sapwood characteristics of Quercus robur +species from the south-western part of the Pannonian +Basin + Jevšenak + Dendrochronologia + 54 + 10.1016/j.dendro.2019.02.006 + 2019 + Jevšenak, J., Goršić, E., Stojanović, +D. B., Matović, B., & Levanič, T. (2019). Sapwood characteristics of +Quercus robur species from the south-western part of the Pannonian +Basin. Dendrochronologia, 54, 64–70. +https://doi.org/10.1016/j.dendro.2019.02.006 + + + Sapwood estimates and the dating of short +ring sequences + Hillam + BAR International Series + 333 + 1987 + Hillam, J., Morgan, R. A., & +Tyers, I. (1987). Sapwood estimates and the dating of short ring +sequences. BAR International Series, 333, +165–185. + + + Estimating missing sapwood rings in three +European gymnosperm species by the heartwood age rule + Gjerdrum + Dendrochronologia + 3 + 31 + 10.1016/j.dendro.2013.03.001 + 2013 + Gjerdrum, P. (2013). Estimating +missing sapwood rings in three European gymnosperm species by the +heartwood age rule. Dendrochronologia, 31(3), 228–231. +https://doi.org/10.1016/j.dendro.2013.03.001 + + + Refinements in the interpretation of +tree-ring dates for oak building timbers in england and +wales + Miles + Vernacular Architecture + 37 + 10.1179/174962906X158291 + 2006 + Miles, D. (2006). Refinements in the +interpretation of tree-ring dates for oak building timbers in england +and wales. Vernacular Architecture, 37, 84–96. +https://doi.org/10.1179/174962906X158291 + + + Bayesian interpretation of tree-ring dates in +practice + Tyers + Vernacular Architecture + 1 + 39 + 10.1179/174962908X365082 + 2008 + Tyers, C. (2008). Bayesian +interpretation of tree-ring dates in practice. Vernacular Architecture, +39(1), 91106. +https://doi.org/10.1179/174962908X365082 + + + A dendrochronology program library in R +(dplR) + Bunn + Dendrochronologia + 2 + 26 + 10.1016/j.dendro.2008.01.002 + 2008 + Bunn, A. G. (2008). A +dendrochronology program library in R (dplR). Dendrochronologia, 26(2), +115–124. +https://doi.org/10.1016/j.dendro.2008.01.002 + + + Statistical and visual crossdating in R using +the dplR library + Bunn + Dendrochronologia + 4 + 28 + 10.1016/j.dendro.2009.12.001 + 2010 + Bunn, A. G. (2010). Statistical and +visual crossdating in R using the dplR library. Dendrochronologia, +28(4), 251–258. +https://doi.org/10.1016/j.dendro.2009.12.001 + + + dplR: Dendrochronology program library in r. R +package version 1.7.4 + Bunn + 2022 + Bunn, A. G., Korpela, M., Biondi, F., +Campelo, F., Mérain, P., Qeadan, F., & Zang, C. (2022). dplR: +Dendrochronology program library in r. R package version 1.7.4. +https://CRAN.R-project.org/package=dplR + + + Bayesian analysis of radiocarbon +dates + Bronk Ramsey + Radiocarbon + 1 + 51 + 10.2458/rc.v51i1.3494 + 2009 + Bronk Ramsey, C. (2009). Bayesian +analysis of radiocarbon dates. Radiocarbon, 51(1), 337–360. +https://doi.org/10.2458/rc.v51i1.3494 + + + A bayesian approach to sapwood estimates and +felling dates in dendrochronology + Millard + Archaeometry + 1 + 44 + 10.1111/1475-4754.00048 + 2002 + Millard, A. (2002). A bayesian +approach to sapwood estimates and felling dates in dendrochronology. +Archaeometry, 44(1), 137–143. +https://doi.org/10.1111/1475-4754.00048 + + + The ups and downs of the building trade in a +medieval city: Tree-ring data as proxies for economic, social and +demographic dynamics in Bruges (c. 12001500) + Haneca + Dendrochronologia + 64 + 10.1016/j.dendro.2020.125773 + 2020 + Haneca, K., Debonne, V., & +Hoffsummer, P. (2020). The ups and downs of the building trade in a +medieval city: Tree-ring data as proxies for economic, social and +demographic dynamics in Bruges (c. 12001500). Dendrochronologia, 64, +125773. +https://doi.org/10.1016/j.dendro.2020.125773 + + + OpenDendro webpages & code + Bunn + 10.5281/ZENODO.6110786 + 2022 + Bunn, A. G., Anchukaitis, K., & +Swetnam, T. L. (2022). OpenDendro webpages & code. Zenodo. +https://doi.org/10.5281/ZENODO.6110786 + + + ggplot2: elegant graphics for data +analysis + Wickham + 2016 + Wickham, H. (2016). ggplot2: elegant +graphics for data analysis. Springer-Verlag. +https://ggplot2.tidyverse.org + + + Correcting the calculation of +gleichläufigkeit + Buras + Dendrochronologia + 34 + 10.1016/j.dendro.2015.03.003 + 2015 + Buras, A., & Wilmking, M. (2015). +Correcting the calculation of gleichläufigkeit. Dendrochronologia, 34, +29–30. +https://doi.org/10.1016/j.dendro.2015.03.003 + + + Beitrag zur rationalisierung eines +dendrochronologischen verfahrens und zur analyse seiner +aussagesicherheit + Eckstein + Forstwissenschaftliches +Centralblatt + 88 + 10.1007/BF02741777 + 1969 + Eckstein, D., & Bauch, J. (1969). +Beitrag zur rationalisierung eines dendrochronologischen verfahrens und +zur analyse seiner aussagesicherheit. Forstwissenschaftliches +Centralblatt, 88, 230–250. +https://doi.org/10.1007/BF02741777 + + + Über die sicherheit jahrringchronologische +datierung + Huber + Holz als Roh und Werkstoff + 10-12 + 6 + 10.1007/BF02603303 + 1943 + Huber, B. (1943). Über die sicherheit +jahrringchronologische datierung. Holz Als Roh Und Werkstoff, 6(10-12), +263–268. https://doi.org/10.1007/BF02603303 + + + On the similarity of tree-ring patterns: +Assessing the influence of semi-synchronous growth changes on the +Gleichläufigkeitskoeffizient for big tree-ring data sets + Visser + Archaeometry + 1 + 63 + 10.1111/arcm.12600 + 2021 + Visser, R. M. (2021). On the +similarity of tree-ring patterns: Assessing the influence of +semi-synchronous growth changes on the Gleichläufigkeitskoeffizient for +big tree-ring data sets. Archaeometry, 63(1), 204–215. +https://doi.org/10.1111/arcm.12600 + + + RemembeRINGs. The development and application +of local and regional tree-ring chronologies of oak for the purposes of +archaeological and historical research in the netherlands + Jansma + 1995 + Jansma, E. (1995). RemembeRINGs. The +development and application of local and regional tree-ring chronologies +of oak for the purposes of archaeological and historical research in the +netherlands. ROB. +https://dspace.library.uu.nl/handle/1874/45149 + + + A simple crossdating program for tree-ring +research + Baillie + Tree-Ring Bulletin + 33 + 1973 + Baillie, M. G. L., & Pilcher, J. +R. (1973). A simple crossdating program for tree-ring research. +Tree-Ring Bulletin, 33, 7–14. + + + Methods for summarizing radiocarbon +datasets + Bronk Ramsey + Radiocarbon + 6 + 59 + 10.1017/RDC.2017.108 + 2017 + Bronk Ramsey, C. (2017). Methods for +summarizing radiocarbon datasets. Radiocarbon, 59(6), 1809–1833. +https://doi.org/10.1017/RDC.2017.108 + + + Radiocarbon calibration and analysis of +stratigraphy: The OxCal program + Bronk Ramsey + Radiocarbon + 2 + 37 + 10.1017/S0033822200030903 + 1995 + Bronk Ramsey, C. (1995). Radiocarbon +calibration and analysis of stratigraphy: The OxCal program. +Radiocarbon, 37(2), 425–430. +https://doi.org/10.1017/S0033822200030903 + + + Summary of dendro data formats (published as +supplementary material for Brewer, Murphy & Jansma, 2011. TRiCYCLE: +a universal conversion tool for digital tree-ring data). + Brewer + Tree-Ring Research + 67 + 10.3959/2010-12.1 + 2011 + Brewer, P., & Murphy, D. (2011). +Summary of dendro data formats (published as supplementary material for +Brewer, Murphy & Jansma, 2011. TRiCYCLE: a universal conversion tool +for digital tree-ring data). Tree-Ring Research, 67, 60. +https://doi.org/10.3959/2010-12.1 + + + Inference from large sets of radiocarbon +dates: software and methods + Crema + Radiocarbon + 10.1017/RDC.2020.95 + 2020 + Crema, E. R., & Bevan, A. (2020). +Inference from large sets of radiocarbon dates: software and methods. +Radiocarbon, 1–17. +https://doi.org/10.1017/RDC.2020.95 + + + Seeing the forest for the trees: New +approaches and challenges for dendroarchaeology in the 21st +century + Domínguez-Delmás + Dendrochronologia + 62 + 10.1016/j.dendro.2020.125731 + 2020 + Domínguez-Delmás, M. (2020). Seeing +the forest for the trees: New approaches and challenges for +dendroarchaeology in the 21st century. Dendrochronologia, 62, 125731. +https://doi.org/10.1016/j.dendro.2020.125731 + + + European Larch Sapwood: A Model for +Predicting the Cambial Age and for a More Accurate +Dating + Shindo + Dendrochronologia + 83 + 10.1016/j.dendro.2023.126150 + 2024 + Shindo, L., Saulnier, M., Raese, H., +Guibal, F., Edouard, J.-L., Bolka, M., Carrer, M., Corona, C., Gassmann, +P., Grabner, M., Guillet, S., Nicolussi, K., Nola, P., Pignatelli, O., +& Stoffel, M. (2024). European Larch Sapwood: A Model for Predicting +the Cambial Age and for a More Accurate Dating. Dendrochronologia, 83, +126150. +https://doi.org/10.1016/j.dendro.2023.126150 + + + + + + diff --git a/joss.06716/10.21105.joss.06716.pdf b/joss.06716/10.21105.joss.06716.pdf new file mode 100644 index 0000000000..55e9a689ad Binary files /dev/null and b/joss.06716/10.21105.joss.06716.pdf differ diff --git a/joss.06716/paper.jats/10.21105.joss.06716.jats b/joss.06716/paper.jats/10.21105.joss.06716.jats new file mode 100644 index 0000000000..334e04fd63 --- /dev/null +++ b/joss.06716/paper.jats/10.21105.joss.06716.jats @@ -0,0 +1,1153 @@ + + +
+ + + + +Journal of Open Source Software +JOSS + +2475-9066 + +Open Journals + + + +6716 +10.21105/joss.06716 + +fellingdater: a toolkit to estimate, +report and combine felling dates derived from historical tree-ring +series. + + + +https://orcid.org/0000-0002-7719-8305 + +Haneca +Kristof + + + + + +Flanders Heritage Agency, Belgium + + + + +24 +4 +2024 + +9 +97 +6716 + +Authors of papers retain copyright and release the +work under a Creative Commons Attribution 4.0 International License (CC +BY 4.0) +2022 +The article authors + +Authors of papers retain copyright and release the work under +a Creative Commons Attribution 4.0 International License (CC BY +4.0) + + + +R +tree-ring analysis +dendrochronology +sapwood +dendroarchaeology + + + + + + Summary +

Tree-ring dating, or dendrochronology, allows the assignment of + calendar-year dates to growth rings that can be observed on an old + piece of timber. Once a tree-ring series is securely anchored to a + calendar year time scale, the end date of the outermost ring can be + used to estimate the year when the tree was felled.

+

The fellingdater package offers a suite of + functions that can assist dendrochronologists to infer, combine and + report felling date estimates from dated tree-ring series, based on + the presence of partially preserved sapwood or waney edge + (Fig. 1).

+ +

A cross-section of a historical timber from a medieval + roof construction. All ring boundaries are marked, as well as the + heartwood and the partially preserved sapwood.

+ + + + + Background +

Dendrochronology is the most precise chronometric dating technique + for (pre-)historical wooden constructions and objects + (Baillie, + 1995). It involves recording the ring width pattern on a + cross-section of an ancient wooden element and matching this pattern + to absolutely dated reference chronologies. This allows anchoring the + recorded tree-ring pattern to an absolute time scale. In + archaeological, architectural or art-historical studies, the primary + objective of a dendrochronological survey is to ascertain an accurate + estimate of the felling date (or dying-off) of the parent + tree from which the timber originates + (Domínguez-Delmás, + 2020; + Haneca + et al., 2009; + Tegel + et al., 2022). This felling date is the closest related and + datable event to the creation of the wooden object or + construction.

+

The exact felling date can be inferred from the most recently + formed tree ring prior to the felling or death of the tree. Often, the + wood of the felled tree has undergone processing, trimming, or + biological deterioration leading to the irreversible loss of wood + tissue. In such cases, the timing of the felling date can only be + estimated. The most challenging situation is when neither sapwood, nor + the transition between heartwood and sapwood, remains on the object or + timber (Fig. 1, + HW/SW boundary). Then, an untraceable amount of wood and growth layers + has been removed and the last measured ring only provides an earliest + possible felling date or terminus post quem.

+

The fellingdater package aims to facilitate + the process to infer, combine and report felling date estimates from + dated tree-ring series, based on the presence of (partially) preserved + sapwood or waney edge.

+ + + Statement of need +

Many descriptive statistics and statistical models have been + published to establish accurate estimates of the expected number of + sapwood rings + (Bleicher + et al., 2020; + Bräthen, + 1982; + Edvardsson + et al., 2022; + Gjerdrum, + 2013; + Haneca + et al., 2009; + Hillam + et al., 1987; + Hollstein, + 1965, + 1980; + Hughes + et al., 1981; + Jevšenak + et al., 2019; + Miles, + 1997; + Pilcher, + 1987; + Rybnicek + et al., 2006; + Shindo + et al., 2024; + Sohar + et al., 2012; + Wazny, + 1990). These models are based on counts of sapwood rings from + living and historical timbers and often rely on log-transformation of + the original data, or use regression models including additional + variables such as mean ring width, the cambial age of the tree or a + combination of both. A standardized methodology for reporting felling + dates is therefore hampered by this variety in statistical + approaches.

+

A Bayesian method to improve the procedures to model sapwood data, + compute lower and upper limits for the felling date based upon the + selected sapwood model and a given credible interval have been + introduced by Millard + (2002). + This procedure was further refined by Miles + (2006), + and critically reviewed with real-life examples by Tyers + (2008). + This workflow has been incorporated in + OxCal, + the routine software for radiocarbon dating and modelling + (Bronk + Ramsey, 2009). Tree-ring analysis, on the other hand, relies on + a growing set of R-packages, with the ‘Dendrochronology + Program Library in R’ + (Bunn, + 2008, + 2010; + Bunn, + Korpela, et al., 2022), at its core (https://opendendro.org/, + Bunn, + Anchukaitis, et al., 2022). Yet, the reporting of felling dates + is currently not a standardized procedure incorporated in an + R-package.

+

The fellingdater package allows to fully + document the methodology to establish a felling date – for a single + timber or a group of timbers – making the whole procedure reproducible + and assists in building standardized workflows when applied to large + datasets (e.g. + Haneca + et al., 2020). The package includes functions related to each + step in the (generalized) workflow when analysing historical tree-ring + series (Fig. 2).

+ +

A generalized workflow and related functions, for + inferring felling dates from tree-ring dated historical + timbers.

+ + + + + Data within the package +

The package comes with published datasets of sapwood counts, + retrieved from their original publication (e.g. + Haneca + & Debonne, 2012). This was only possible for a limited + number of datasets as many have been published as histograms with wide + bins (>1), what does do not allow to retrieve the underlying data + points. An overview of all included sapwood datasets is generated by + sw_data_overview().

+

More information on the datasets, such as the bibliographic + reference to the original publication, the wood species and some basic + descriptive statistics can be accessed by + sw_data_info(<name_of_dataset>).

+

sw_model() fits a chosen density + distribution to the original data, and returns the output of the + modelling process. With sw_model_plot() the + model is visualized as a ggplot-style graph + (Wickham, + 2016) (Fig. + 3).

+ library(fellingdater) + +sw_data_overview() +#> [1] "Brathen_1982" "Hollstein_1980" "Miles_1997_NM" "Miles_1997_SC" +#> [5] "Miles_1997_WBC" "Pilcher_1987" "Sohar_2012_ELL_c" "Sohar_2012_ELL_t" +#> [9] "Sohar_2012_FWE_c" "Sohar_2012_FWE_t" "Wazny_1990" "vanDaalen_NLBE" +#> [13] "vanDaalen_Norway" + +model <- sw_model("Hollstein_1980", plot = FALSE) +sw_model_plot(model) + +

Two sapwood datasets with a fitted density function to + the raw data.

+ + + + + Example of use + + Installation +

The latest version is hosted on + GitHub + and + R-universe.

+ pak::pak("ropensci/fellingdater") + +# or + +install.packages("fellingdater", repos = "https://ropensci.r-universe.dev") + + + Reading tree-ring files +

The function read_fh() is an extension to + the dplR::read.fh() function and allows to + read .fh + (format + Heidelberg) files of ring widths (in decadal, half-chrono + or chrono format) + (Brewer + & Murphy, 2011). The function is focused on extracting + information found in the HEADER fields of the .fh files, which often + harbour essential information necessary for establishing a well + informed estimate of the felling date. The + read_fh() function retrieves the information + from the HEADER fields and lists the items as attributes to the + ring-width measurements. The + fh_header()function facilitates easy + conversion to a data.frame.

+ + + Crossdating +

The function cor_table() computes commonly + used correlation values between dated tree-ring series and reference + chronologies. This function helps to verify the assigned end date of + the series by comparing the measurements against absolutely dated + reference chronologies, thereby providing information on timber + provenance. The latter enables the selection of the most appropriate + sapwood model for the tree-ring data.

+

The correlation values computed are:

+ + +

glk: ‘Gleichläufigkeit’ or ‘percentage of parallel variation’ + (Buras + & Wilmking, 2015; + Eckstein + & Bauch, 1969; + Huber, + 1943; + Visser, + 2021).

+ + +

glk_p: significance level associated with the glk-value + (Jansma, + 1995).

+ + +

r_pearson: the Pearson’s correlation coefficient.

+ + +

t_St: Student’s t-value based on + r_pearson.

+ + +

t_BP: t-values according to the algorithm + proposed by Baillie & Pilcher + (1973).

+ + +

t_Ho: t-values according to the algorithm + proposed by Hollstein + (1980).

+ + + Doel1_trs <- read_fh(Doel1, header = FALSE) +Hollstein_crn <- read_fh("Hollstein80.fh", header = FALSE) + +cor_table(x = Doel1_trs, + y = Hollstein_crn, + min_overlap = 80, + output = "table", + sort_by = "t_BP") + + + Felling date interval +

After selecting the appropriate sapwood model (e.g., one of + Fig. 3) one can use the + model to estimate the upper and lower limits of the number of + missing sapwood rings. The function + sw_interval() calculates the probability + density function (PDF) and highest probability density interval + (HDI) of the felling date range based on the observed number of + sapwood rings (n_sapwood = ...), their + chronological dating (last = ...), and the + selected sapwood data (sw_data = ...) and + model (densfun = ...).

+

In the example below, 10 sapwood rings were observed on a + historical timber (with the last ring dated to 1234 CE) that is + supposed to have a provenance in the Southern Baltic region (covered + by the sapwood model published by Wazny + (1990)). + The HDI delineates an interval in which the actual felling date is + most likely situated (Fig. + 4).

+

Note that the more sapwood rings that have been measured, the + more probability mass is assigned to the tails of the sapwood + model.

+ # 10 sapwood rings observed and the Wazny 1990 sapwood model: + +interval <- sw_interval( + n_sapwood = 10, + last = 1234, + hdi = TRUE, + cred_mass = .95, + sw_data = "Wazny_1990", + densfun = "lognormal", + plot = TRUE) + +

A truncated lognormal distribution, representing the + sapwood model for a tree-ring series with 10 sapwood rings. The + black line delineates the 95% credible interval for the felling + date.

+ + + + + Combine felling dates + + sw_combine +

The procedure to combine felling dates of a group of related + tree-ring series with (partially) preserved sapwood, in order to + narrow down the range of a shared felling date, is provided by the + function sw_combine(). This function + returns a list with:

+ + +

the probability density function (PDF) for the felling date + of the individual series and the PDF of the model that + combines these individual series + ($data_raw),

+ + +

the HDI for the combined estimate of the common felling + date ($hdi_model),

+ + +

the Agreement index + ($A_model) of the model, expressing how + well the individual series fit into the model,

+ + +

an overview of the felling date range for the individual + series ($individual_series), and their + Agreement index + (Ai) to the combined model.

+ + +

The function sw_combine_plot() allows to + visualize the output.

+

The rationale and mathematical background of the + Agreement index (Ai) + was introduced and developed by Bronk Ramsey + (1995, + 2017). + Both the Ai of the individual series + and for the whole model (Amodel) + should ideally be around 100%, and not lower than the critical + threshold Ac = 60%.

+

The example dataset below consists of 5 dated tree-ring series, + one of which has an exact felling date + (Fig. 5, + left). The proposed combined felling date equals the + felling date of the series with an exact felling date (trs_15), + but now it can be assessed that this falls within the felling date + ranges for three other individual series (trs_11, trs_12 and + trs_14). One other series (trs_13) has no remaining sapwood and + therefore only an earliest possible felling date can be given + (arrow pointing away from last measured ring). The agreement + indexes of all individual series and the overall model are high + and above the critical threshold of 60%.

+ trs_example2 +#> series last n_sapwood waneyedge +#> 1 trs_11 1000 5 FALSE +#> 2 trs_12 1005 10 FALSE +#> 3 trs_13 1008 NA FALSE +#> 4 trs_14 1000 1 FALSE +#> 5 trs_15 1010 3 TRUE + +p1 <- sw_combine(trs_example2, plot = TRUE) + +

Graphical output of + sw_combine(). The sapwood model for the + individual series in light grey, the probability density + function of the combined felling in dark grey tone. The credible + interval for the felling date of individual series is shown as a + dashed red line and a black line for the combined estimate. The + dataset in the left graph includes an exact felling date that + matches with the estimates for the other series. The graph on + the right shows a model that fails to group all series around a + common felling date.

+ + +

In the next example, an attempt to compute a common felling + date for a group of 5 tree-ring series fails. All but one of the + series include partially preserved sapwood, but these tree-ring + series do not share a common timing for their estimated felling + date (Fig. 5, + right). The agreement index of the model is far below 60%, + as is the case for most of the individual series.

+ trs_example4 +#> series last n_sapwood waneyedge +#> 1 trs_21 1000 5 FALSE +#> 2 trs_22 1005 10 FALSE +#> 3 trs_23 1005 NA FALSE +#> 4 trs_24 1020 1 FALSE +#> 5 trs_25 1040 0 FALSE + +p2 <- sw_combine(trs_example4, plot = TRUE) + + + + Sum felling dates +

For large datasets of dated tree-ring series, it is not always + straightforward to assess temporal trends in the frequency of + felling dates. The individual series each have their own probability + density function based on a chosen sapwood model and the number of + observed sapwood rings. To make another reference to radiocarbon + dating, it is common practice in the analysis of large volumes of + radiocarbon dates to compute the summed probability + densities (SPD) of the calibrated radiocarbon dates. Summed + probabilities are used to determine the temporal density of ages + (events) in situations where there is no clear prior information on + their distribution + (Bronk + Ramsey, 2017). This procedure is implemented in OxCal and the + R-package rcarbon + (Crema + & Bevan, 2020). The function + sw_sum() makes his procedure available for + tree-ring analyses. The summed probability distribution (SPD) of the + individual probability densities of felling dates of single + tree-ring series with incomplete sapwood allows visualizing of + fluctuations in the incidence of potential felling dates over time. + Exact felling dates derived from tree-ring series with waney edge + are not included in the computational process of the SPD as they + would result in anomalous spikes in the SPD, since their associated + probability (p = 1) would be assigned to a single + calendar year. Therefore exact felling dates are plotted separately + on top of the SPD (Fig. + 6).

+ sum <- sw_sum(trs_example7) + +sw_sum_plot(sum, dot_size = 2, dot_shape = 25) + +

Graphical representation of the out put of + sw_sum(). The blue bars represent the + summed probability density (SPD) of the individual series with + partial sapwood. The red line is a rectangular filter applied to + the SPD to highlight the general trend. Series with exact felling + dates are plotted as triangles.

+ + + + + + Future work +

In its current version, the package + fellingdater is tailored to the general + workflow for analyzing tree-ring datasets from wooden cultural + heritage objects and constructions, made of European oak + (Quercus sp.). The sapwood data included in the + current version reflect this focus on oak. However, all functions can + also work with a custom sapwood dataset provided as a + data.frame. As such, sapwood data from other + regions and wood species can also be explored, modeled and used to + determine felling dates.

+ + + Acknowledgements +

Koen Van Daele and Ronald Visser fueled me with valuable feedback + on earlier versions of the package.

+

At rOpenSci, dr. Antonio J. Pérez-Luque, dr. + Nicholas Tierney and dr. Maëlle Salmon provided an essential and + constructive software review, allowing me to significantly improve the + quality of the package.

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