Calculate_MCMC_growth_curve {BayesGrowth}

Calculate_MCMC_growth_curve

Description

A 'stan.fit' object produced from Estimate_MCMC_Growth is converted to a dataframe and structured using requested quantiles. This function takes the list of MCMC results for multiple chains, restructures them into a dataframe and calculates quantiles around length-at-age estimates. The quantiles are produced using the tidybayes::mean_qi() function and this result is returned from the function. This can be conveniently plotted in a ggplot using the geom_lineribbon() function provided in the tidybayes package.

Usage

Calculate_MCMC_growth_curve(
  obj,
  Model = NULL,
  max.age = NULL,
  probs = c(0.5, 0.75, 0.95)
)

Arguments

obj

An output from the Estimate_MCMC_Growth function

Model

The model used in the Estimate_MCMC_Growth object. Either "VB", "Gom" or "Log".

max.age

The max age to estimate growth up until.

probs

The percentiles of the results to return. Can be a single value or a vector of values. A single quantile width is required rather than its range. For example, 50th percentiles would be width = .5 which would return a lower percentile at .25 and an upper percentile of .75.

Value

A tibble that has been formatted using tidybayes::mean_qi(). This includes variables: Age, LAA, .lower, .upper, .width, .point and .interval.

Examples

# load example data
data("example_data")
## Biological info - lengths in mm
max_size <- 440
max_size_se <- 5
birth_size <- 0
birth_size_se <- 0.001 # an se cannot be zero

# Use the function to estimate the rstan model
fit <- Estimate_MCMC_Growth(data = example_data,
                            Model = "VB" ,
                            iter = 5000,
                            Linf = max_size,
                            Linf.se = max_size_se,
                            L0 = birth_size,
                            sigma.max = 100,
                            L0.se = birth_size_se,
                            k.max = 1,
                            n_cores = 1)

# Use function to return a dataframe of model predictionsfor VB growth model
Calculate_MCMC_growth_curve(fit, Model = "VB" , max.age = max(example_data$Age))