Man pages for ada-w-yan/reassortment
Modelling Evolution of Strain Mixtures Including Reassortment
| apply_named_args | a version of apply() that matches the dimnames of X to the... |
| enumerate_popn | take a vector with the number of virions of each strain, and... |
| get_hash | get short hash of current commit |
| get_user_options | specify user options for cluster |
| get_vars_from_list_with_check | extract variables from list, throwing an error if they are... |
| lapply_w_name | a version of lapply() that supplies FUN with both the name... |
| list_vars_from_environment | gather variables with given names from an environment into a... |
| make_and_package_segments | returns the number of newly produced virions after... |
| make_mutation_matrix | make matrix of probabilities of strain x mutating into strain... |
| make_results_folder | make folder to store results and (optional) store hash of... |
| mutate_popn_wrapper | make function to mutate a population of virions |
| normalise | normalises a vector so that it sums to 1 |
| num2str | turn number(s) into string for filename, replacing decimal... |
| parLapply_wrapper | wrapper for parLapply for cluster |
| plot_multirun_segments | plot results of run_xxx_model by segment when there are... |
| plot_multirun_strains | plot results of run_xxx_model by strain when there are... |
| plot_segments | plot results of run_xxx_model by segment |
| plot_strains | plot results of run_xxx_model by strain |
| probabilistic_round | round a (vector of) numbers up with probability equal to... |
| reassort_popn | old implementation of reassortment |
| round_preserve_sum | rounds a numeric vector probabilistically such that its sum... |
| run_default_pars | Simulate evolution of mixture by reassortment and/or... |
| run_mutation_model_no_coinfection | Simulate evolution of mixture by mutation, with no... |
| segments_to_strain | turns a list of segment indices into a strain number |
| sensitivity_plot | plot proportion of each strain at 20 generations across... |
| setup_cluster | Cluster setup |
| simulate_evolution | Simulate evolution of mixture by reassortment and/or mutation |
| sum_strains | takes a vector of length equal to the number of virions,... |
| vnapply | vapply returning numeric vector of length 1 |
