Build a taphonomic decay Markov chain (DTMC)

A discrete-time absorbing Markov chain over decomposition stages. From each transient stage a body either progresses one step toward the terminal "skeletal" state (ordinary decay) or diverts to the terminal "mummified" state (preserved). A preservation factor – the desiccant/bacteriocidal effect of quicklime, aridity, sealing – shifts mass from progression toward diversion, so a high-lime interment routes the body to "mummified" rather than "skeletal". Compare the natural (preservation = 0) chain against a treated one to quantify how much the burial practice changes the fate distribution.

Usage

morie_taphonomy_decay_chain(
  preservation = 0,
  decay_rate = 0.5,
  mummify_rate = 0.5,
  states = c("fresh", "bloat", "active", "advanced")
)

Arguments

preservation

Preservation factor in [0, 1]: 0 = ordinary decay, higher = stronger diversion toward mummification.

decay_rate

Base per-step progression probability in (0, 1] (default 0.5).

mummify_rate

Base per-step diversion-to-mummified probability in [0, 1] (default 0.5); scaled by preservation.

states

Character vector of transient decomposition stages (default c("fresh", "bloat", "active", "advanced")).

Value

A named list: P (row-stochastic transition matrix, double), states, transient, absorbing (c("skeletal", "mummified")), and preservation.

See also

morie_taphonomy_decay_absorption, morie_taphonomy_decay_simulate, morie_taphonomy_decay_delta

Examples

ch <- morie_taphonomy_decay_chain(preservation = 0.7)
round(ch$P, 3)
#>           fresh bloat active advanced skeletal mummified
#> fresh       0.5  0.15   0.00     0.00     0.00      0.35
#> bloat       0.0  0.50   0.15     0.00     0.00      0.35
#> active      0.0  0.00   0.50     0.15     0.00      0.35
#> advanced    0.0  0.00   0.00     0.50     0.15      0.35
#> skeletal    0.0  0.00   0.00     0.00     1.00      0.00
#> mummified   0.0  0.00   0.00     0.00     0.00      1.00