impliedTimescales: Implied timescales of a Markov chain

In markovchain: Easy Handling Discrete Time Markov Chains

Implied timescales of a Markov chain

Description

Computes the implied relaxation timescale associated with each non-trivial eigenvalue of a finite, irreducible discrete-time Markov chain.

Usage

impliedTimescales(object)

## S4 method for signature 'markovchain'
impliedTimescales(object)

Arguments

object

A markovchain object representing a finite, irreducible discrete-time Markov chain.

Details

For a row-stochastic transition matrix P with eigenvalues 1=\lambda_1,\lambda_2,\ldots,\lambda_n (|\lambda_1| the unique unit eigenvalue of an irreducible chain), the implied timescale of \lambda_k, k>1, is

\tau_k = -\frac{1}{\log|\lambda_k|}

for 0<|\lambda_k|<1. Each \tau_k measures how many steps the mode associated with \lambda_k takes to decay by a factor of 1/e; larger timescales correspond to slower-decaying, more persistent modes.

Only irreducibility is required, not aperiodicity: this is the same convention used by slem and spectralGap, and it lets impliedTimescales() document periodic and boundary cases explicitly rather than rejecting them:

• If |\lambda_k| is (numerically) exactly 1 – which happens for non-trivial eigenvalues of periodic chains, e.g. \lambda=-1 for a 2-cycle – the corresponding mode never decays and tau_k = Inf is returned. This is a boundary case of the formula above (as |\lambda|\to 1^-, \tau\to\infty) that is handled explicitly rather than by evaluating -1/\log(1), which is numerically -Inf rather than the mathematically correct +Inf.

• If |\lambda_k| is (numerically) exactly 0, the mode decays immediately and tau_k = 0 is returned. log(0) evaluates to -Inf in R, so this case is already handled correctly by the formula itself and needs no special-casing.

The term "implied timescale" follows the Markov state model literature in molecular kinetics, where it is additionally used, across chains estimated at increasing lag times, as a self-consistency check on the Markov (memoryless) approximation: implied timescales that are approximately constant across lag times support the model, while ones that drift indicate it should be revisited (see Prinz et al. (2011)). Building such a lag-time comparison is left to the user, since it requires re-estimating the chain at each lag: impliedTimescales() itself only evaluates a single, already-fitted markovchain object.

The implementation calls eigen() with only.values = TRUE, so it never computes eigenvectors. Its time complexity is O(n^3) and its memory use is O(n^2) for a dense n-state transition matrix. It supports both row- and column-stochastic storage.

Value

A named numeric vector of length n-1 (one entry per non-trivial eigenvalue), sorted by decreasing timescale, i.e. by decreasing eigenvalue modulus. Names are "tau2", "tau3", ..., matching the usual eigenvalue indexing \lambda_2,\lambda_3,\ldots in decreasing modulus. For the trivial one-state chain, a length-zero named numeric vector is returned.

References

Swope, W. C., Pitera, J. W. and Suits, F. (2004). Describing protein folding kinetics by molecular dynamics simulations, 1: Theory. J. Phys. Chem. B, 108(21), 6571-6581.

Prinz, J.-H., Wu, H., Sarich, M., Keller, B., Senne, M., Held, M., Chodera, J. D., Schutte, C. and Noe, F. (2011). Markov models of molecular kinetics: Generation and validation. Journal of Chemical Physics, 134(17), 174105.

See Also

slem, spectralGap, is.irreducible

Examples

statesNames <- c("a", "b")
mc <- new("markovchain",
  states = statesNames,
  transitionMatrix = matrix(c(0.7, 0.3, 0.1, 0.9),
    byrow = TRUE, nrow = 2,
    dimnames = list(statesNames, statesNames)))
impliedTimescales(mc)

markovchain documentation built on Oct. 10, 2026, 9:07 a.m.