# Generated by roxygen2: do not edit by hand

S3method(plot,parameter_sensitivity)
S3method(plot,profile_likelihood)
S3method(plot,topolow_amcs_diagnostics)
S3method(plot,topolow_convergence)
S3method(print,parameter_sensitivity)
S3method(print,profile_likelihood)
S3method(print,topolow)
S3method(print,topolow_amcs_diagnostics)
S3method(print,topolow_convergence)
S3method(summary,topolow)
export(adaptive_MC_sampling)
export(add_noise_bias)
export(analyze_network_structure)
export(c25)
export(c25_claud)
export(c25_old)
export(c25_older)
export(calculate_annual_distances)
export(calculate_cumulative_distances)
export(calculate_diagnostics)
export(calculate_prediction_interval)
export(calculate_procrustes_difference)
export(calculate_procrustes_significance)
export(calculate_weighted_marginals)
export(check_gaussian_convergence)
export(clean_data)
export(coordinates_to_matrix)
export(create_and_optimize_RACMACS_map)
export(create_cv_folds)
export(create_diagnostic_plots)
export(create_topolow_map)
export(dist_to_titer_table)
export(error_calculator_comparison)
export(find_mode)
export(generate_complex_data)
export(generate_synthetic_datasets)
export(generate_unique_string)
export(ggsave_white_bg)
export(increase_na_percentage)
export(initial_parameter_optimization)
export(log_transform_parameters)
export(long_to_matrix)
export(make_interactive)
export(new_aesthetic_config)
export(new_annotation_config)
export(new_dim_reduction_config)
export(new_layout_config)
export(only_virus_vs_as)
export(parameter_sensitivity_analysis)
export(plot_3d_mapping)
export(plot_cluster_mapping)
export(plot_distance_heatmap)
export(plot_network_structure)
export(plot_temporal_mapping)
export(prepare_heatmap_data)
export(process_antigenic_data)
export(profile_likelihood)
export(prune_distance_network)
export(run_adaptive_sampling)
export(save_plot)
export(scatterplot_fitted_vs_true)
export(symmetric_to_nonsymmetric_matrix)
export(unweighted_kde)
export(weighted_kde)
import(ggplot2)
importFrom(MASS,mvrnorm)
importFrom(Racmacs,acmap)
importFrom(Racmacs,keepBestOptimization)
importFrom(Racmacs,optimizeMap)
importFrom(Racmacs,save.coords)
importFrom(Rtsne,Rtsne)
importFrom(ape,dist.nodes)
importFrom(ape,extract.clade)
importFrom(ape,is.rooted)
importFrom(ape,nodepath)
importFrom(ape,unroot)
importFrom(coda,effectiveSize)
importFrom(coda,gelman.diag)
importFrom(coda,mcmc)
importFrom(coda,mcmc.list)
importFrom(data.table,data.table)
importFrom(data.table,fread)
importFrom(data.table,setDT)
importFrom(dplyr,"%>%")
importFrom(dplyr,across)
importFrom(dplyr,all_of)
importFrom(dplyr,distinct)
importFrom(dplyr,filter)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarise)
importFrom(dplyr,summarize)
importFrom(dplyr,ungroup)
importFrom(filelock,lock)
importFrom(filelock,unlock)
importFrom(ggplot2,aes)
importFrom(ggplot2,annotate)
importFrom(ggplot2,coord_fixed)
importFrom(ggplot2,element_blank)
importFrom(ggplot2,element_line)
importFrom(ggplot2,element_rect)
importFrom(ggplot2,element_text)
importFrom(ggplot2,geom_abline)
importFrom(ggplot2,geom_density)
importFrom(ggplot2,geom_hline)
importFrom(ggplot2,geom_line)
importFrom(ggplot2,geom_point)
importFrom(ggplot2,geom_segment)
importFrom(ggplot2,geom_smooth)
importFrom(ggplot2,geom_text)
importFrom(ggplot2,geom_tile)
importFrom(ggplot2,ggplot)
importFrom(ggplot2,ggsave)
importFrom(ggplot2,guide_legend)
importFrom(ggplot2,guides)
importFrom(ggplot2,labs)
importFrom(ggplot2,margin)
importFrom(ggplot2,scale_color_manual)
importFrom(ggplot2,scale_colour_gradient)
importFrom(ggplot2,scale_colour_manual)
importFrom(ggplot2,scale_fill_gradient)
importFrom(ggplot2,scale_fill_manual)
importFrom(ggplot2,scale_shape_manual)
importFrom(ggplot2,scale_x_continuous)
importFrom(ggplot2,scale_y_continuous)
importFrom(ggplot2,theme)
importFrom(ggplot2,theme_classic)
importFrom(ggplot2,theme_minimal)
importFrom(ggplot2,theme_void)
importFrom(ggplot2,unit)
importFrom(ggrepel,geom_label_repel)
importFrom(ggrepel,geom_text_repel)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,colors)
importFrom(graphics,hist)
importFrom(grid,arrow)
importFrom(grid,unit)
importFrom(gridExtra,grid.arrange)
importFrom(igraph,components)
importFrom(igraph,get.edgelist)
importFrom(igraph,graph_from_adjacency_matrix)
importFrom(igraph,graph_from_data_frame)
importFrom(igraph,is_connected)
importFrom(igraph,layout_with_fr)
importFrom(lhs,maximinLHS)
importFrom(parallel,clusterEvalQ)
importFrom(parallel,clusterExport)
importFrom(parallel,detectCores)
importFrom(parallel,makeCluster)
importFrom(parallel,mclapply)
importFrom(parallel,parLapply)
importFrom(parallel,stopCluster)
importFrom(plotly,ggplotly)
importFrom(plotly,layout)
importFrom(reshape2,melt)
importFrom(rgl,axes3d)
importFrom(rgl,open3d)
importFrom(rgl,plot3d)
importFrom(rgl,rgl.close)
importFrom(rgl,rgl.cur)
importFrom(rgl,rgl.snapshot)
importFrom(rlang,sym)
importFrom(scales,comma)
importFrom(scales,label_number)
importFrom(stats,aggregate)
importFrom(stats,approx)
importFrom(stats,bw.SJ)
importFrom(stats,bw.bcv)
importFrom(stats,bw.nrd)
importFrom(stats,bw.nrd0)
importFrom(stats,bw.ucv)
importFrom(stats,coef)
importFrom(stats,complete.cases)
importFrom(stats,cor)
importFrom(stats,cov)
importFrom(stats,dist)
importFrom(stats,dnorm)
importFrom(stats,hclust)
importFrom(stats,lm)
importFrom(stats,mad)
importFrom(stats,median)
importFrom(stats,na.omit)
importFrom(stats,optimize)
importFrom(stats,prcomp)
importFrom(stats,qt)
importFrom(stats,quantile)
importFrom(stats,qunif)
importFrom(stats,residuals)
importFrom(stats,rnorm)
importFrom(stats,runif)
importFrom(stats,sd)
importFrom(stats,setNames)
importFrom(stats,var)
importFrom(tools,file_ext)
importFrom(umap,umap)
importFrom(utils,globalVariables)
importFrom(utils,read.csv)
importFrom(utils,tail)
importFrom(utils,write.csv)
importFrom(utils,write.table)
importFrom(vegan,procrustes)
importFrom(vegan,protest)
