v1.3.9

[tokami]

New features

• A spin-up (burn-in) period can be specified using inp$nspinup in number
  of time steps. It helps stabilise the fit in cases where only catches
  are available in the beginning of the time series.

Minor changes

• On load, spict checks if the currently available TMB version is the same
  as the one that was used to install spict. Gives warning if there is a
  mismatch.
• The harvest control rule (HCR) labeled "ices" in the manage() function was
  updated to be in line with the HCR recommended to be used by ICES in 2025.
• The management section of the guidelines vignette was updated to be in line
  with current recommendations by ICES (state 2025).

Bug fixes

• intermediatePeriodCatchList is now used by the manage function, previously was
  ignored
• The retrospective peels generated by the retro() function did not behave as
  expected. In some cases (e.g., with mid-year index timing), the most recent
  index observations were not removed as intended. This issue has been fixed and
  tested across a range of catch and index timing configurations, using both
  annual and quarterly catch observations. The updated implementation follows
  the convention that each peel reproduces the data availability in the
  assessment year; for example, if an index observation is available in the
  assessment year but catch data are not, the same pattern is replicated in each
  peel.