Man pages for ELAplus
Energy Landscape Analysis for Ecological Communities
| baseabtable | Abundance table for 16 taxa across 256 samples |
| basemetadata | Environmental metadata for 256 samples |
| Bi | Bi |
| bin2id | bin2id: map a binary vector to a 64base characters |
| bootstrap_ELA | Energy landscape analysis with bootstrap resampled SA results |
| bootstrap_SA | Parameter fitting with bootstrap sampling of datasets |
| deltaE_histogram | Plot histograms of bootstrap deltaE values |
| DisconnectivityGraph | DisconnectivityGraph: Generate a disconnectivity graph |
| ELA | Energy landscape analysis in parallel mode |
| ELAplus-package | Energy Landscape Analysis for Ecological Communities |
| ELPruning | ELPruning |
| Energy | Energy |
| Findbp | Search best hyperparameters for SA fitting (lambda and weight... |
| Formatting | Formatting |
| GELAObj | GELAObj |
| GradELA | GradELA |
| GradientDescent | Gradient descent estimation of model parameters |
| gStability | gstability |
| hb.paramgen | Randomly generate model parameters for heat-bath sampling |
| HeatBath | Heat-bath sampling of binary states |
| id2bin | id2bin: map a 64base characters to a binary vector |
| MinTippingPath | MinTippingPath |
| OnestepHBS | Perform one heat-bath update step |
| PCplot | PCplot:Scatter plot of community compositions colored by... |
| plotSAtest | plotSAtest: plot the results of SA fitting (Findbp output) |
| runSA | Stochastic approximation for parameter fitting |
| sa2params | Convert SA output to model parameter objects |
| saEndpoint | Extract endpoint parameters from runSA output |
| showDG | showDG: draw DisconnectivityGraph |
| showGELA3D | GELA3D: draw 3D plot of energy landscape |
| showIntrGraph | showIntrGraph: draw interaction matrix on a PCoA plot |
| showSSD | showSSD: draw stable state diagram |
| showSSD_ggplot | showSSD_ggplot: draw stable state diagram using ggplot |
| SSentropy | SSentropy |
| sstable | sstable |
| Stability | stability |
| SteepestDescent | SteepestDescent |
| tptable | tptable |
