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AquaticLifeHistory

DOI R-CMD-check

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:

Installation

You can install the released 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)

#> $VonB
#>         Parameter           SE
#> Linf 2439.5652138 50.416331766
#> k       0.1253499  0.006938586
#> L0    659.2971929 14.318722887
#> RSE    97.9461196           NA
#> 
#> $Logistic
#>         Parameter          SE
#> Linf 2163.8640309 26.46867817
#> g       0.2894532  0.01039625
#> L0    727.0885234 13.58771346
#> RSE   110.3850532          NA
#> 
#> $Gompertz
#>        Parameter           SE
#> Linf 2250.136998 32.621706305
#> g       0.207524  0.008455423
#> L0    695.603478 13.779414070
#> RSE   103.855273           NA
#> 
#> $AIC
#>   Model    AICc AIC diff Weight
#> 1    VB 3535.10     0.00      1
#> 2   Log 3605.40    70.30      0
#> 3   Gom 3569.54    34.45      0

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)
#>     Estimate        SE
#> A50 13.95113 0.3033328
#> A95 16.53427 0.5321205

# 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

browseVignettes("AquaticLifeHistory")

These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.