In jonathansmart/AquaticLifeHistory: Life History Analysis Tools

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AquaticLifeHistory

AquaticLifeHistory allows users to undertake fisheries life history analyses using contemporary approaches as simple R functions. These analyses currently include length-at-age modelling using a multi-model approach, estimating age-at-maturity and length-at-maturity. The main package functions are:

Estimate_Growth() performs length-at-age analyses using a von Bertalanffy growth model, Gompertz model and/or Logistic model.
Estimate_Age_Maturity() Estimates age-at-maturity using either binomial maturity or proportion mature data and age.
Estimate_Len_Maturity() Estimates age-at-maturity using either binomial maturity or proportion mature data and length.

Installation

You can install the latest released version from CRAN with:

install.packages("AquaticLifeHistory")

You can install the development version of AquaticLifeHistory from Github with:

# install.packages("devtools")
devtools::install_github("jonathansmart/AquaticLifeHistory")

Usage

Perform growth analysis

library(AquaticLifeHistory)

# load example data set
data("growth_data")

# Run function with three default model candidates.
# Model parameters, AIC values are returned and a plot with bootstrapped CI's is printed to examine fits.
Estimate_Growth(growth_data)

Perform age-at-maturity analysis

# load example data set
data("maturity_data")

# Run function to estimate age-at-maturity parameters
Estimate_Age_Maturity(maturity_data)

# A plot can also be returned with bootstrapped CI's.
Estimate_Age_Maturity(maturity_data, return = "plot")

For further examples of these and other functions use the provided vignettes