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rebuild: Rebuilding Analysis Functions

Consolidated R package containing functions from FLRebuild and rebuild packages needed for fisheries stock rebuilding analysis workflows.

Installation

# Install from local source
devtools::install("flr/rebuild")

Purpose

This package consolidates all functions needed for rebuilding analysis, eliminating the need to source multiple files from different packages. All functions previously sourced in analysis scripts are now available through a single package.

Functions Included

Core Functions:

  • toLogits(), fromLogits() - Steepness parameter transformations
  • ftmb(), ftmb2(), ftmb3() - Stock-recruitment relationship fitting
  • updateRefs() - Update reference points
  • pellatParams(), pellatParamFn() - Pella-Thompson production model parameters
  • abi(), abiAge(), abiMsy() - Age-based indicators
  • processError() - Process error calculation
  • covarFn(), leslieFn() - Life history and demographic covariates
  • invSRR(), refCreate(), rmax(), rmsy(), rvirgin() - Stock-recruitment reference points

Rebuilding Analysis:

  • Rebuilding trajectory functions (rebuild(), rebuildTime(), etc.)
  • Pella-Tomlinson model functions
  • Bootstrap and rebuilding analysis functions

Usage

library(rebuild)

# All functions are now available without sourcing
library(FLCore)
library(FLBRP)

# Example: Fit stock-recruitment relationship
# sr <- ftmb2(flsr_object, spr0 = 0.7)

# Example: Update reference points
# brp <- updateRefs(brp_object)

# Example: Calculate covariates
# covars <- covarFn(brp_object)

Breaking Changes

⚠️ Version 0.1.0 includes breaking changes:

  • from_logits() → fromLogits()
  • to_logits() → toLogits()

See NEWS.md for migration guide.

Package Status

This package consolidates functions from FLRebuild and rebuild packages. As of version 0.1.0, this package is self-contained and has no dependencies on FLCandy or FLRebuild packages.