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KyuriP/causalnet
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causalnet is an R package for enumerating and analyzing directed causal networks derived from an undirected orpartially directed skeleton. It includes:
- Enumeration of all orientation-consistent digraphs (honors one-way and bidirectional constraints via
fixed_edges). - Feedback-loop detection.
- Topology summaries (loop count, degree variability, node-overlap score, average loop size) with ggplot visuals.
- Dynamic simulation of node states via Euler–Maruyama SDEs
– built-innonlinear model (default),linear, or acustom update;
– optional exogenous stress inputstress_event(t, state);
– boundary handling:"reflect","clamp","none", or"auto".
install.packages("remotes")remotes::install_github("KyuriP/causalnet")
library(causalnet)## 1) Undirected skeleton (triangle)adj<-matrix(0,3,3,dimnames=list(paste0("X",1:3), paste0("X",1:3)))adj[1,2]<-adj[2,1]<-1adj[2,3]<-adj[3,2]<-1adj[3,1]<-adj[1,3]<-1## 2) Enumerate all directed variants (allowing bidirected edges)nets<- generate_directed_networks(adj,allow_bidirectional=TRUE)## 3) Summarize structuresummary_df<- summarize_network_metrics(nets)plot_network_metrics(summary_df,n_bins=6)# cowplot grid of 4 panels## 4) Pick two representativesi_no_loop<- which(summary_df$num_loops==0)[1]i_max_loop<- which.max(summary_df$num_loops)## 5) Simulate dynamics with a brief external stress at t ∈ [0, 5]params<- get_sample_parameters(n_nodes= nrow(adj))stress_event<-function(t,state)if (t<=5) rep(0.01, length(state))else rep(0, length(state))S_no<- simulate_dynamics(nets[[i_no_loop]],params,t_max=20,dt=0.05,stress_event=stress_event)S_hi<- simulate_dynamics(nets[[i_max_loop]],params,t_max=20,dt=0.05,stress_event=stress_event)## 6) Plot trajectories (stress windows use the *time* axis)plot_dynamics(S_no,stress_windows=list(c(0,5)),title="No Loops")plot_dynamics(S_hi,stress_windows=list(c(0,5)),title="Many Loops")
A full walk-through (enumeration → metrics → simulation → visuals) is available in the Quarto vignette:
quarto::quarto_preview("vignettes/causalnet_demo.qmd")
Issues & feature requests: please use the tracker →https://github.com/KyuriP/causalnet/issues.
When filing a bug, include aminimal reproducible example (reprex), yoursessionInfo(), and the package version.Questions / ideas: open a Discussion or an Issue.
Pull requests welcome: add a short description, tests (if applicable), and updated docs where relevant.
This project is released under theGPL-3 license.
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