Update paper.md

scollinselliott · scollinselliott · commit 664ac9e6033f · 2025-06-30T17:49:19.000-04:00
diff --git a/paper/paper.md b/paper/paper.md
@@ -19,7 +19,7 @@ bibliography: ../inst/REFERENCES.bib
 
 # Summary
 
-Archaeological chronology-building centers on two types of dates, absolute and relative. Absolute dates are associated with a calendrical date (even approximate), and relative refer to events only known via relationships to others (before/after). Relative events are then associated to absolute via contextual or logical associations. E.g, a _terminus post quem_ (_t.p.q._) of a datable coin found in a soil deposit ensures the deposit came after the production of the coin. Applying probabilistic methods to chronology has traditionally centered on radiocarbon dating, but the broader goal of extending formal methods to all aspects of chronology necessitate a way to address artifact typologies. Artifacts largely persist in being dated by qualitative judgment (e.g, "around the start of the 4th century BCE"). Typologies yet constitute a major chronological component, and their production and use transcend assumptions about depositional sequences (e.g., finds can be made elsewhere and well before a site is occupied). Moreover, typologies are in a constant state of revision and adjustment, such that the dates of types can differ according to authority. The reasons why a type is dated the way it is (i.e., which sites, deposits, and their comparisons inform its date) can also become opaque, such that investigators inherently resist chronological revisions in order to assess the bibliography on any one type (on this conservatism, see @rotroff_four_2005, 20). This situation further presents a challenge for any researcher applying statistical methods to archaeological chronologies with artifacts, as one must make _ad hoc_ and often awkward decisions about dates of types, resulting in what @lavan_checklist_2021[15] called "abonimable" chronologies. 
+Archaeological chronology-building centers on two types of dates, absolute and relative. Absolute dates are associated with a calendrical date (even approximate), and relative refer to events only known via relationships to others (before/after). Relative events are then associated to absolute via contextual or logical associations. E.g, a _terminus post quem_ (_t.p.q._) of a datable coin found in a soil deposit ensures the deposit came after the production of the coin. Applying probabilistic methods to chronology has traditionally centered on radiocarbon dating, but the broader goal of extending formal methods to all aspects of chronology necessitate a way to address artifact typologies. Artifacts largely persist in being dated by qualitative judgment (e.g, "around the start of the 4th century BCE"). Typologies yet constitute a major chronological component, and their production and use transcend assumptions about depositional sequences (e.g., finds can be made elsewhere and well before a site is occupied). Moreover, typologies are in a constant state of revision and adjustment, such that the dates of types can differ according to authority. The reasons why a type is dated the way it is (i.e., which sites, deposits, and their comparisons inform its date) can also become opaque, such that investigators inherently resist chronological revisions in order to assess the bibliography on any one type (on this conservatism, see @rotroff_four_2005[20]). This situation further presents a challenge for any researcher applying statistical methods to archaeological chronologies with artifacts, as one must make _ad hoc_ and often awkward decisions about dates of types, resulting in what @lavan_checklist_2021[15] called "abonimable" chronologies. 
 
 The `R` package `eratosthenes` (named after Eratosthenes of Cyrene, author of the _Chronographiai_) provides functions for chronology-building, above all to bring artifact dating within the scope of formal mathematical estimation. Hence, an investigator can obtain separate probability density functions (p.d.f.) for the production, use, and deposition of an artifact type, in addition to marginal p.d.f.s for all relative sequential events (howsover determined) and absolute constraints (howsoever defined). It uses Gibbs sampling, by now a conventional Markov Chain Monte Carlo method in archaeological chronology [@geman_stochastic_1984; @buck_bayesian_1996]. In particular, a two-step routine of Gibbs sampling is performed, the first a preliminiary sampler to select a starting date, and a second main sampler that uses consistent batch means (CBM) as a stopping rule, given that convergence in distribution is assured [@jones_fixed-width_2006; @flegal_markov_2008]. Full reporting on the Monte Carlo standard errors (MCSE) is provided, giving a concrete error in +/- years for each marginal density. Finally, `eratosthenes` provides functions for assessing the level of dependence of events upon each other within the structure of joint conditional density. Changes in artifact dates brought about by any change in the structure of a chronology can therefore be readily evaluted.
 
@@ -68,7 +68,7 @@ For the purposes of illustration, an initial application was undertaken for a sm
 
 ![Marginal p.d.f.s of 2 depositional events and 5 shipwrecks from the Mediterraenan, given the joint conditional contained in [eda20250628](https://github.com/scollinselliott/eratosthenes-data/tree/main/data/20250628). The wreck Grand Congloué A is earlier than the traditional date: future datasets will work to revise sequencing and constraints.\label{fig2}](fig2.png)
 
-The sack of Carthage has also been a key point for dating a particular type of ceramic transport container, the [Dressel 1 amphora type](https://archaeologydataservice.ac.uk/archives/view/amphora_ahrb_2005/details.cfm?id=324). Since it has not be found in pre-destruction layers of that site, the start of its production has been dated to the later part of the 2nd century BCE [@tchernia_vin_1986,42]. Rather than just relying on one site, however, the entire set of conditional events in `eda20250628` yield a density for its production, use, and deposition (Fig. \autoref{fig3}). One can change the inputs to assess if and how its dates shfit around. The shipwreck at Isla Pedrosa, for example, evidenced Dressel 1B containers, which [@parker_ancient_1992,217-218] suggested were spurious. If one asserts a finds relationship between Dressel 1B the Isla Pedrosa wreck, the dates of its production, use, and deposition will be drawn heavily toward the mid-2nd c. BCE. For assessing which events are the most determinative in dating the Dressel 1B type, squared displacement is computed, which, for this dataset, show that the Madrague de Giens shipwreck has the greatest impact on shifting the type's date ($\delta^2 = 5.16\text{E}06; \alpha = -5000, \omega = 1950$; the full table is given [here](https://github.com/scollinselliott/eratosthenes-data/tree/main/data/20250628)).
+The sack of Carthage has also been a key point for dating a particular type of ceramic transport container, the [Dressel 1 amphora type](https://archaeologydataservice.ac.uk/archives/view/amphora_ahrb_2005/details.cfm?id=324). Since it has not be found in pre-destruction layers of that site, the start of its production has been dated to the later part of the 2nd century BCE [@tchernia_vin_1986,42]. Rather than just relying on one site, however, the entire set of conditional events in `eda20250628` yields a density for its production, use, and deposition (Fig. \autoref{fig3}). Changing the relationships and associations in the inputs will naturally change the resulting estimatin of the type. The shipwreck at Isla Pedrosa for example evidenced Dressel 1B containers, which @parker_ancient_1992[217-218] suggested were spurious. If one asserts a finds relationship between Dressel 1B the Isla Pedrosa wreck, the dates of its production, use, and deposition will be drawn heavily toward the mid-2nd c. BCE. In this respect, squared displacement will provide an overview of which events are the most determinative. For this dataset, the Madrague de Giens shipwreck has the greatest impact on shifting the date of the Dressel 1B type ($\delta^2 = 5.16\text{E}06; \alpha = -5000, \omega = 1950$; the full table is given [here](https://github.com/scollinselliott/eratosthenes-data/tree/main/data/20250628)).
 
 ![P.d.f.s of the production, use, and deposition of the Dressel 1B type amphora, using the "naive" production rule and given the joint conditional contained in [eda20250628](https://github.com/scollinselliott/eratosthenes-data/tree/main/data/20250628).\label{fig3}](fig3.png)
 
