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docs: correct coalescent-opt and skyline CLI help #861

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17 changes: 11 additions & 6 deletions packages/treetime/src/commands/timetree/args.rs
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Expand Up @@ -120,15 +120,20 @@ pub struct TreetimeTimetreeArgs {

/// Optimize coalescent time scale Tc to maximize coalescent likelihood.
///
/// When set, TreeTime will find the optimal Tc using Brent's method. This is similar
/// to Python v0's `--coalescent=opt`, but uses a closed-form solution.
#[cfg_attr(feature = "clap", clap(long, conflicts_with = "coalescent", conflicts_with = "coalescent_skyline"))]
/// When set, TreeTime computes the closed-form maximum-likelihood estimate
/// Tc = I / M directly, where I is the pairwise-merger-rate integral over the
/// tree and M is the number of mergers. There is no iterative search and no
/// initial guess. This corresponds to Python v0's `--coalescent=opt`.
#[cfg_attr(
feature = "clap",
clap(long, conflicts_with = "coalescent", conflicts_with = "coalescent_skyline")
)]
pub coalescent_opt: bool,

/// Use skyline coalescent model instead of constant Tc.
///
/// Estimates a piecewise linear coalescent rate history. Requires --n-skyline to specify
/// the number of grid points.
/// Estimates a piecewise-constant coalescent time scale Tc(t). Requires --n-skyline to specify
/// the number of segments.
#[cfg_attr(feature = "clap", clap(long))]
#[cfg_attr(
feature = "clap",
Expand All @@ -138,7 +143,7 @@ pub struct TreetimeTimetreeArgs {

/// Number of grid points in skyline coalescent model.
///
/// Only used when --coalescent-skyline is set. Defines how many piecewise linear segments
/// Only used when --coalescent-skyline is set. Defines how many piecewise-constant segments
/// are used to model Tc(t) over time. Must be at least 2.
#[default = 10]
#[cfg_attr(feature = "clap", clap(long, default_value_t = TreetimeTimetreeArgs::default().n_skyline))]
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