# Generated by roxygen2: do not edit by hand

S3method(as.data.frame,hrri_arch)
S3method(print,hrri_arch)
S3method(print,hrri_arch_validation)
S3method(print,hrri_benchmark)
S3method(print,rri_accuracy)
S3method(summary,hrri_arch)
export(attach_hrri_ids)
export(benchmark_hrri)
export(hrri_infer_architecture)
export(plot_RRI_ternary)
export(plot_hrri_benchmark)
export(plot_rri_accuracy)
export(plot_rri_properties)
export(plot_rri_recovery_landscape)
export(plot_rri_recovery_map)
export(plot_rri_simulation_demo)
export(plot_rri_state_space)
export(plot_rri_timeseries)
export(plot_rri_validation)
export(rri_accessible_capacity)
export(rri_accuracy)
export(rri_capacity_index)
export(rri_compensation_index)
export(rri_connectivity_score)
export(rri_default_reservoirs)
export(rri_domain_influence)
export(rri_kinetics_score)
export(rri_latent_correlation)
export(rri_memory_index)
export(rri_micro_functional_score)
export(rri_o2_demand)
export(rri_pipeline)
export(rri_pipeline_st)
export(rri_property_scores)
export(rri_recovery_metrics)
export(rri_reference_scores)
export(rri_root_physio)
export(rri_sensitivity)
export(rri_simulation_demo)
export(simulate_redox_holobiont)
export(theme_ems)
export(validate_architecture)
importFrom(ggplot2,
  aes,
  after_stat,
  annotate,
  coord_equal,
  coord_fixed,
  coord_flip,
  element_blank,
  element_rect,
  element_text,
  facet_wrap,
  geom_abline,
  geom_col,
  geom_density,
  geom_histogram,
  geom_hline,
  geom_line,
  geom_point,
  geom_text,
  geom_tile,
  geom_vline,
  ggplot,
  labs,
  margin,
  scale_color_manual,
  scale_colour_manual,
  scale_colour_viridis_c,
  scale_fill_gradientn,
  scale_fill_manual,
  scale_fill_viridis_c,
  scale_fill_viridis_d,
  scale_y_continuous,
  theme,
  theme_classic,
  theme_minimal
)
importFrom(graphics,
  abline,
  legend,
  lines,
  matplot,
  mtext,
  par,
  plot
)
importFrom(igraph,
  centr_degree,
  cluster_fast_greedy,
  ecount,
  edge_attr,
  global_efficiency,
  is_directed,
  modularity,
  simplify,
  transitivity,
  vcount
)
importFrom(rlang,.data)
importFrom(stats,
  aggregate,
  ave,
  coef,
  complete.cases,
  cor,
  cov,
  lm,
  median,
  nls,
  nls.control,
  pnorm,
  prcomp,
  predict,
  quantile,
  rlnorm,
  rnbinom,
  rnorm,
  runif,
  sd,
  setNames,
  var,
  vcov
)
importFrom(tidyr,pivot_longer)
importFrom(tidyselect,all_of)
importFrom(utils,
  combn,
  globalVariables,
  head,
  modifyList,
  packageVersion,
  tail
)
