| add_columns | Add derived variables to a dataframe |
| add_relative_time | Add relative time column to a dataframe, and diversity at the... |
| adjust_mig_rate | Two-dimensional adjusted migration rate |
| all_output | Create a composite dataframe for a batch of simulations,... |
| all_statuses | Return the final line (or an earlier line) of every error log... |
| ancestry | Get the ancestry of each genotype |
| apply_combinations | Apply a function to every combination of some sequences |
| apply_combinations_parallel | Apply a function to every combination of some sequences... |
| combine_dfs | Combine (and optionally process) data for one simulation |
| corCI_high | Function to return the upper bound of the confidence interval... |
| corCI_low | Function to return the lower bound of the confidence interval... |
| cor_pval | Function to return the p.value of a two.sided test, using the... |
| cor_summary | Correlations between diversities and "outcome" |
| count_drivers | Count the number of ancestors of a node in a phylogenetic... |
| count_parameters | Count the number of parameters in a parameter file in a... |
| count_seeds | Count the number of rows in a dataframe per parameter set. |
| create_plots_batch | Create image files for every simulation in a batch |
| data | Example dataframe combining output from many simulations |
| depth_wait_cor_summary | Correlations between diversities and "waiting_time" for... |
| disp_rate | Expected disperal speed for migration model |
| disp_rate_demon | Demon dispersal rate |
| disp_rate_fission | Dispersal speed for deme fission model |
| disp_rate_max | Maximum limit on dispersal speed for migration model |
| disp_rate_min | Minimum limit on dispersal speed for migration model |
| dominant | Find the latest-occurring mutation shared by at least a... |
| driver_geno_div_df_batch | Create a data frame of genotype diversity versus time for a... |
| driver_matrix | Example relatedness matrix |
| driver_phylo | Example phylogeny dataframe |
| filter_by_generation_or_numcells | Filter a data frame by Generation or NumCells |
| final_error_message | Return the final line (or an earlier line) of an error log of... |
| final_generation | Return the final generation number of a simulation |
| find_correlations | Generic function to find a correlation between two columns of... |
| first_inc_moment | Get the first incomplete moment from frequency data |
| geno_dist | Get genotype frequencies in increasing order of size |
| get_cor_summary | Generate summary dataframe of correlations with "outcome" |
| get_summary | Get summary metrics for one or more simulations |
| get_tree_from_matrix | Get a "phylo" object from a relatedness matrix |
| get_Variable_cor_summary | Generate summary dataframe of correlations with the variable... |
| get_Variable_cor_summary_FinalSize | Generate summary dataframe of correlations with the variable... |
| get_wait_cor_summary | Generate summary dataframe of correlations with... |
| grid_plot | Plot a grid from a properly formatted data frame. |
| hist2 | Alternative to base hist function (using dplyr) |
| image_df_from_grid_file | Read a file containing grid states and process it into a... |
| inv_Simpson_index | Calculate the inverse Simpson index |
| lambda | Expected migration rate per deme |
| lambda_invasion | Rate of migration followed by survival |
| make_dir | Create a directory name including parameter names and values |
| make_image_file_name | Create an image file name including parameter names and... |
| metrics | Calculate average number of ancestors per node (n) and... |
| mig_rate | Demon migration rate |
| muller_df_from_file | Read a "phylo" dataframe and process it for plotting |
| output | Example output dataframe |
| output_allele_counts | Example allele counts dataframe |
| output_driver_allele_counts | Example driver allele counts dataframe |
| output_driver_genotype_counts | Example driver genotype counts dataframe |
| output_genotype_counts | Example genotype counts dataframe |
| output_passengersgrid | Example grid |
| parameter_names_and_values | Find the names and final values of parameters that were... |
| parameters | Example parameters file |
| plot_all_charts | Plot a set of charts representing allele frequencies and... |
| plot_allelecount_vs_origintime | Plot allele count versus origin time |
| plot_all_images | Create a set of grid and Muller plots |
| plot_corr_outcome_versus_period | Plot correlation between outcome and diversity, versus... |
| plot_corr_waiting_time_versus_depth | Plot correlations between waiting time and diversity measured... |
| plot_corr_waiting_time_versus_start_size | Plot correlation between waiting time and diversity, versus... |
| plot_counts | Plot counts of variant allele frequencies on linear scales |
| plot_cum_dist | Plot cumulative density of variant allele frequencies versus... |
| plot_curves_faceted | Plot relationship between two variables faceted by K (rows)... |
| plot_driver_geno_div | Plot genotype diversity versus time |
| plot_figure2 | Create a set of plots for Figure 2 |
| plot_first_inc_moment | Plot first incomplete moment from frequency data |
| plot_logit_freq_dist | Plot a histogram of variant allele frequencies with logit... |
| plot_mutation_waves | Plot numbers of cells with n mutations for each value of n |
| plot_R2_verus_sweep_metric | Plot R-squared versus mean sweep metric |
| plot_scatter_outcome_diversity | Example scatter plots of outcome versus diversity |
| plot_scatter_waiting_time_diversity | Example scatter plots of waiting time versus diversity |
| plot_trajectories_by_diversity | Plot growth trajectories, coloured by driver edge diversity |
| plot_trajectories_by_K | Plot growth trajectories, coloured by K |
| plot_tree | Plot a phylogenetic tree |
| plot_viol_sweep_metric | Violin plot of mean sweep metric (genotype frequency... |
| prob_successful_migration | For cells at the boundary of a population, find mean... |
| quadratic_diversity | Rao's quadratic diversity, using a binary distance measure,... |
| read_delim_special | Attempt to read a tab-delimited file and return the contents,... |
| reflect_on_diagonal | Reflect a matrix on its leading diagonal (useful if distance... |
| refresh_data_files | Don't use this; it's just for refreshing data files on Rob's... |
| rho | Probability of fixation in a Moran process |
| sum_df | Example summary data |
| summary | Summary data for many simulations |
| sweep_sequence | Calculate how the genotype frequency distribution changes... |
| sweep_times | Find generations at which sweeps (or at least partial sweeps)... |
| T_grow_j | Moran growth waiting time |
| time_expected | Migration waiting time (any population size) |
| time_fixation | Conditional fixation time |
| time_migration | Migration waiting time from fully occupied deme |
| trans_rate | Moran process transition rates |
| wait_cor_summary | Correlations between diversities and "waiting_time" |
