Man pages for TheoPannetier/comrad
R implementation of a Competitive Radiation model
| apply_mutations | Apply random mutations to a community |
| apply_speciation | Resolve speciation in a comrad community |
| build_spp_tbl | Extracts phylogenetic information from a 'comrad' simulation |
| check_dd_model_is_avail | Check that the requested DD model is available in 'DDD' |
| ddd_optimizer | Optimizer functions from package DDD |
| dd_func_colours | Colours associated with each DD function |
| dd_func_names | Names of the DD functions |
| dd_loglik_func | Log-likelihood function of a diversity-dependent model given... |
| dd_model_colours | Colours associated with each DD model |
| dd_model_comrad_to_ddd | Values of 'DDD' argument 'ddmodel' corresponding to 'comrad'... |
| dd_model_lc | Diversity-dependent model with linear (l) dependence on... |
| dd_model_ll | Diversity-dependent model with linear (l) dependence on... |
| dd_model_lp | Diversity-dependent model with linear (l) dependence on... |
| dd_model_lx | Diversity-dependent model with linear (l) dependence on... |
| dd_model_names | Names of DD models implemented in 'comrad' |
| dd_model_pc | Diversity-dependent model with power (p) dependence on... |
| dd_model_pl | Diversity-dependent model with power (p) dependence on... |
| dd_model_pp | Diversity-dependent model with power (p) dependence on... |
| dd_model_px | Diversity-dependent model with power (p) dependence on... |
| dd_models | List of all diversity-dependent models |
| dd_model_to_extinction_func | Find DD extinction function associated with a DD model |
| dd_model_to_speciation_func | Find DD speciation function associated with a DD model |
| dd_model_xc | Diversity-dependent model with exponential (x) dependence on... |
| dd_model_xl | Diversity-dependent model with exponential (x) dependence on... |
| dd_model_xp | Diversity-dependent model with exponential (x) dependence on... |
| dd_model_xx | Diversity-dependent model with exponential (x) dependence on... |
| default_params_doc | Documentation for main parameters of the model |
| default_pars | Default parameter values |
| draw_comm_next_gen | Draw a new community from the current one |
| draw_init_params_dd_ml | Draw a set of initial parameter values for a DD model |
| draw_nb_offspring | Draw a number of offspring given a fitness value |
| exclude_ephemeral_spp | Exclude ephemeral species |
| find_trait_gaps | Find gaps in trait values |
| fit_dd_model_with_fossil | Fit a diversity-dependent diversification model to... |
| fit_dd_model_without_fossil | Fit a diversity-dependent diversification model to... |
| fitness_func | Fitness functions |
| get_carrying_cap | Get the carrying capacity for a given trait value |
| get_comp_coeff_comm | Get the competition coefficients between an individual and... |
| get_dnltt | Compute the delta nLTT between two trees |
| get_edge_tbl | Get a table with node and edge info |
| get_fitness | Compute fitness values |
| get_fitness_landscape | Compute the fitness along a range of trait values, given a... |
| get_ltt_tbl | Get a lineage-through-time table |
| get_n_eff | Compute the effective population size |
| get_root_age | Get the age of the root of a tree |
| has_brute_force_opt | Are brute force options available? |
| interpolate_ltt | Interpolate LTT for a given time sequence |
| ltt_tbl_to_func | Transform the LTT table into a step function |
| pipe | Pipe operator |
| plot_aicw_pie | Plot Akaike weights as a pie chart |
| plot_comm_bubbles | Plot population densities and trait distribution over time,... |
| plot_comm_size | Plot community size over generations |
| plot_comm_trait_evolution | Plot the evolution of trait values in the community over... |
| plot_comm_traits | Plot trait distribution in a generation |
| plot_comm_traits_anim | Plot an animation of trait distribution through generations |
| plot_compare_dd_functions | Quickly compare the three diversity-dependent functions |
| plot_dd_func_colours | Plot a key to the colours used to represent DD functions |
| plot_dd_model_colours | Plot a key to the colours used to represent DD models |
| plot_fitness_landscape | Plot the fitness landscape at a given time in the simulation |
| plot_fitness_landscape_evol | Plot the fitness landscape in a 'comrad' simulation over time |
| plot_trait_disparity | Plot trait disparity over time |
| rand_comm | Sample a random 'comrad' community |
| rates_from_dd_model | Get speciation and extinction rates values given a DD model... |
| rates_from_exp_dist | Estimate diversity-dependent rates from mean parameter of the... |
| read_comrad_tbl | Read simulation data |
| run_simulation | Run the simulation |
| set_sampling_freq | Set default sampling frequency |
| sim_to_phylo | Convert 'comrad' simulation results into a phylogeny |
| simulate_dd_phylo | Simulate a phylogeny with a diversity-dependent birth-death... |
| sort_by_ref | Sort a vector by ascending value |
| stem_or_crown | Find wheter origin is stem or crown lineages |
| summarise_aicw_over_trees | Average AICw scores over all replicate trees |
| summarise_waiting_times | Summarise waiting times data set |
| testargs | Assert a function argument is of correct type |
| transform_pars | Transforming parameters from -Inf to Inf into parameters from... |
| untransform_pars | Untransforming parameters from -1 to 1 into parameters from... |
| waiting_times | Extract times to events from a phylogeny |
| write_newick_str | Convert a species history table to a Newick string |
