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admtools

INFRA · APIS
Velocity0.0

Estimate and Manipulate Age-Depth Models

github.com/mindthegap-erc/admtools ↗

The age-depth engine under a small stratigraphy stack, growing one adapter at a time

stratigraphyage-depth-modelspaleobiologyinteroperabilitys3-classes
◆Current state
admtools estimates and manipulates age-depth models, with the generics time_to_strat() and strat_to_time() as the transformation layer a small stratigraphy stack is built on. Since 0.1.0 it has accumulated the S3 vocabulary that work needs — sac for sediment accumulation curves, timelist and stratlist for time- and height-associated data — and then adapters outward: pre_paleoTS for StratPal and paleoTS in 0.4.0, FossilSim taxonomy and fossils objects in 0.5.0, and age-to-time transformation for FossilSim in 0.6.0. Version 0.5.0 also added what it calls basic functionality for depth-depth models alongside the age-depth ones.
◆Where it's heading
This package moves in step with StratPal, from the same group: admtools 0.4.0 shipped its pre_paleoTS transformations fifty-seven minutes before StratPal released the class itself, and both took on FossilSim within a month of each other in spring 2025. The pattern is consistent — establish generics, define classes, then connect to whatever package the field already uses. The depth-depth work is the one thread pointing inward rather than outward, and it is still described as basic.
◆Prediction
Depth-depth models are the obvious thing to finish, since they mirror age-depth machinery the package already has; expect any release here to be shadowed by a matching change in StratPal within weeks either side.

◆Recent moves

  1. 1y ago

    Age-to-time transformation for FossilSim integration

    Adds transformation between age and time for FossilSim, plus a vignette covering the connection. It completes the integration begun a month earlier and follows StratPal's own FossilSim work by two months.

    View source ↗
  2. 1y ago

    Depth-depth models and FossilSim object transformations

    Two directions at once: transformation of FossilSim taxonomy and fossils objects between time and stratigraphic domains, and a first cut at depth-depth models alongside the age-depth ones the package is named for. The depth-depth line is the more interesting of the two — it mirrors the existing machinery for a second problem — but the notes claim only basic functionality.

    View source ↗
  3. 1y ago

    pre_paleoTS transformations and age-depth model anchoring

    Adds transformations for the pre_paleoTS class to link with StratPal and paleoTS, and anchoring of age-depth models. Stamped fifty-seven minutes before the StratPal release that introduced the class, which is how tightly these two packages are developed.

    View source ↗
  4. 1y ago

    More sedimentation-rate generator options and sac utilities

    Extends sed_rate_from_matrix(), abstracts the extraction of tie points, and adds utility functions for the sac class. Interior consolidation of the vocabulary the adapters later depend on.

    View source ↗
  5. 2y ago

    timelist and stratlist classes; unified transformation syntax

    Defines the timelist and stratlist S3 classes for data tied to time or height, unifies the syntax for time-depth transformation, and drops the ape dependency. The syntax unification is what makes the later adapter releases short.

    View source ↗
  6. 2y ago

    Multiple tie points, sedimentation-rate estimation and the sac class

    Expands estimation to multiple tie points, adds estimation of sedimentation rates and the sac class for sediment accumulation curves, and supports phylo objects. The release where the package became more than the two transformation generics it started with.

    View source ↗