The biogrowth package includes two functions for
making simulations including parameter uncertainty:
predict_growth_uncertainty() and the generic
predictMCMC(). The former includes parameter uncertainty
considering that the model parameters follow a normal distribution with
known mean and variance (defined on different scales). The latter, uses
the Markov Chain of a model fitted using an MCMC algorithm to propagate
the uncertainty in the parameter estimates.
Although these functions account for parameter uncertainty in the
model predictions, they do not allow the definition of custom
distribution for the model parameters. Nonetheless, that is relatively
simple to do using the
predict_growth() function together
with the functions from the tidyverse.
First, we need to define the growth model to use and the time points
where the solution is to be calculated. This is done in the same way as
a “usual” calculation in
Next, we need to define the parameter sample. The
tibble() function provides a convenient way for this. In
this example, we will use 500 iterations, considering that \(\log N \sim Normal(0,1)\), \(\mu \sim Gamma(3,5)\) and \(\lambda \sim Gamma(2,2)\) with \(C=6\) constant.
set.seed(12412) niter <- 500 par_sample <- tibble(logN0 = rnorm(niter, mean = 0, sd = 1), C = 6, mu = rgamma(niter, shape = 3, rate = 5), lambda = rgamma(niter, shape = 2, rate = 2)) par_sample %>% pivot_longer(everything()) %>% ggplot() + geom_histogram(aes(value)) + facet_wrap("name", scales = "free") #> `stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
pmap() function from purrr provides
a convenient way to convert the parameter sample to a list that defines
the model and we can pass to
predict_growth() using the
map() function (also from purrr).
Now, it is just a question of post-processing the simulations. For instance, we can calculate summary statistics of the simulations at each time point.
…that can be plotted using