rmse_sample: Lowest-RMSE sample from time series

In gheysenemma/microsimR: A Simulator Package with a collection of basic community models that outputs count data of microbial communities

Description

Computes the Root Mean Square Error between subsequent generations (columns) in given species abundances matrix (time series) as a measure of convergence. The timepoint with the lowest RMSE-difference with respect to the previous timepoint is then extracted and a normalised sample is returned (proportions).

Usage

rmse_sample(spab, warn = TRUE, norm = TRUE, cutoff = 1e-04)

Arguments

spab	Species abundances matrix with OTUs in the rows and the timepoints as columns.
warn	default TRUE, set to FALSE to suppress convergence warning
norm	default TRUE: compute RMSE on compositional time series (abundances per time point sum to 1)
cutoff	The value the minimum RMSE cannot exceed in order to declare convergence.

Value

A sample vector with the length equal to the number of rows of given input species abundances matrix.

Examples

spab <- glv(N = 10, A = powerlawA(n = 10, alpha = 1.2), tend = 10000)
sample <- rmse_sample(spab)

gheysenemma/microsimR documentation built on Dec. 20, 2021, 10:46 a.m.