Man pages for EvoLandEco/eve
Evolution Emulator, phylogenetically dependent
| bind_raw | bind_raw |
| bind_replication | bind_replication |
| calculate_CI_alt | Calculating confidence interval for LTT plot (reversed time... |
| check_folder | check_folder |
| check_path | check_path |
| download_ftp_file | Function to batch download files from an 'FTP' or 'SFTP'... |
| draw_daughter_lineages | Draw the state history of two daughter edges connected to a... |
| edd_combo_maker | Making a parameter space for edd simulation |
| edd_fetch | Function to fetch simulation files from an 'FTP' or 'SFTP'... |
| edd_fetch_logs | Function to fetch log files from an 'FTP' or 'SFTP' server. |
| edd_fetch_results | Function to fetch simulation results from an 'FTP' or 'SFTP'... |
| edd_go | Starting a edd simulation |
| edd_load | edd_load |
| edd_load_split | edd_load_split |
| edd_merge | edd_merge |
| edd_plot | Generating plots for a replicated edd simulation |
| edd_plot_balance | Generating boxplots of tree balance indices |
| edd_plot_branch | Generating boxplots of various tree branching measures |
| edd_plot_eds | Generating line plot of evolutionary distinctiveness of each... |
| edd_plot_grouped_eds | Generating line plot of evolutionary distinctiveness of each... |
| edd_plot_grouped_las | Generating line plot of speciation rates of each lineage by... |
| edd_plot_grouped_ltt | Generating LTT plot for a replicated edd simulation |
| edd_plot_grouped_mus | Generating line plot of extinction rates of each lineage by... |
| edd_plot_grouped_temporal_dynamics | Generating plots of grouped temporal dynamics of a single... |
| edd_plot_las | Generating line plot of speciation rates of each lineage |
| edd_plot_ltt | Generating LTT plot for a replicated edd simulation |
| edd_plot_mus | Generating line plot of extinction rates of each lineage |
| edd_plot_nltt | Generating nLTT plot for a replicated edd simulation |
| edd_plot_stats | Generating boxplots of tree statistics |
| edd_plot_temporal_dynamics | Generating plots of temporal dynamics of a single simulation |
| edd_plot_tree | Plotting a tree for a selected parameter set |
| edd_sim | Function to simulate the evolutionary distinctiveness... |
| edd_sim_batch | edd_sim_batch |
| edd_sim_rep | edd_sim_rep |
| edd_stat | Function to calculate tree statistics of simulation results |
| edd_stat_rtree | Function to calculate tree statistics of search_tree results |
| extract_which | extract_which |
| job_detail | Parsing log files in a folder into a list of job details |
| job_parameter | Find out which parameter set is used for a job |
| job_status | Parsing log files in a folder into a matrix of job status |
| L2ED | Converting a table with speciation and extinction events to... |
| L2ED_cpp | C++ version of L2ED |
| L2NND | Converting a table with speciation and extinction events to... |
| L2Phi | Converting a table with speciation and extinction events to a... |
| L2Phi_cpp | C++ version of L2Phi #' @description Function to convert a... |
| L2phylo2 | Function to convert a table with speciation and extinction... |
| list_files_ftp | Function to list files on an FTP or SFTP server. |
| l_to_newick_ed | Convert an reverse-timescale L table to newick format string |
| l_to_phylo_ed | Convert an reverse-timescale L table to phylo object, only... |
| match_raw | match_raw |
| match_time_step | match_time_step |
| match_which | match_which |
| phylo2mpd | Converting a phylogenetic tree of phylo object to mean... |
| phylo2pd | Converting a phylogenetic tree of phylo object to total... |
| reduce_element | reduce_element |
| sample2 | Takes samples in the usual manner |
| save_result | save_result |
| search_tree | Function to search for trees with a given number of tips and... |
| stat_histree | Mapping historical states to a phylo tree |
| swap_layers | swap_layers |
| upload_to_ftp | Function to upload a files to an FTP or SFTP server. |
