An R package to implement some of the methods of empirical dynamic modelling
The name pbsEDM combines our workplace, the Pacific Biological Station (PBS) in British Columbia, Canada, with empirical dynamic modelling (EDM), the focus of the package. The package was developed in conjuction with a manuscript currently being submitted.
The package implements the simplex and S-map algorithms of empirical dynamic modelling, and creates visualisations to help understand the methods, for example:
Users can also analyse their own data. The package should not really be used yet until the associated manuscript is reviewed (and the package will be more understandable in conjunction with the manuscript). However, it can be installed directly from GitHub with
install.packages("devtools") # One-time installation if you don't already have devtools
devtools::install_github("pbs-assess/pbsEDM")
The vignettes are already rendered here:
- analyse_simple_time_series.html How to analyse a simple time series using the simplex algorithm, and produce figures that help understand the algorithm.
- aspect_2.html Demonstration of Aspect 2.
- aspect_3_4.html Demonstrations of Aspects 3 and 4.
- pbsSmap.html Demonstration of S-map code.
The source code written in Rmarkdown, the R code that gets extracted from the
Rmarkdown code, and the resulting .html files are all found within your library
folder (where all your R libraries get saved), in
library\pbsEDM\doc\. Or you can look at the vignettes\ folder on GitHub or locally.
Just run the following code. Type the function name (or look at the help with ?<function_name>) to see what it does.
E_results <- pbsEDM_Evec(NY_lags_example$N_t)
plot_pbsEDM_Evec_save(E_results) # Figure 1
plot_explain_edm_save(E_results[[1]]) # Figure 2
plot_rho_Evec_save() # Figure 3
plot_library_size_save() # Figure 4
# Animated figures for the Appendix:
plot_pbsEDM_Evec_movie_save(E_results) # Figure S.1
plot_explain_edm_movie_save(E_results[[1]]) # Figure S.2
plot_explain_edm_all_tstar_movie_save(E_results[[1]]) # Figure S.3