Man pages for sams25/rcombinator_old
Tools to Simulate the Evolution of Genetic Sequences
| burst_copies | Chooses how much to burst a sequence by That is, how much to... |
| choose_pairing | Chooses two numbers randomly (with repitition possible) from... |
| compare_all | Function to compare simulations without recombination and... |
| convert_init_dist_to_df | Prints summary statistics for distances to initial sequence... |
| copy_number_evolution | Simulates the copy number evolution for a set of transposons... |
| copy_number_growth | To model copy number variation over time |
| cumulate_distribution | Converts a probability distribution into a cumulative... |
| cumulate_matrix | Converts a transition matrix into a 'cumulative transition... |
| dist_to_data_frame | Helper function for plotting Converts a distance matrix into... |
| find_paramater_balance_copy_number_variation | To find a balance between various parameters that results in... |
| full_pipeline_comparison | Full pipeline for simulation of retrotransposon evolution |
| get_distance_to_initial_timestep | Prints summary statistics for distances to initial sequence... |
| get_k80_matrix | Chooses a transition matrix according the Kimura-80 model |
| get_random_sequence | Creates many copies of a random DNA sequence of a prescribed... |
| get_summary_stats | Prints summary statistics for distances between sequences |
| get_summary_stats_timestep | Prints summary statistics for distances between sequences for... |
| kill_copies | Selects a set of sequences randomly given the max copy number... |
| normalise_distribution | Normalises a distribution from 0 to 1 given the relative... |
| pairwise_distances | Gets pairwise distances from the sequence data of a Point... |
| pairwise_distances_bursts | Gets pairwise distances from the sequence data when burst... |
| pairwise_distances_timestamp | Gets pairwise distances from the sequence data at a... |
| pick_random_event | Takes a probability distribution of events and returns which... |
| plot_pairwise_data | Prints pairwise data over time from a data frame of sequence... |
| plot_pairwise_data_complex | Plots the pairwise distances for a matrix of strings |
| plot_sequence_counts | To plot sequence counts over time |
| plot_summary_stats | Plots summary statistics for distances between sequences |
| plot_summary_stats_complex | Plots summary statistics for distances between sequences |
| point_mutation_nucleotide | Mutates a nucleotide according to some model Takes a... |
| point_mutation_sequence | Mutates an entire subsequence according to a given transition... |
| point_mutation_sequences | Mutates a list of sequences according to some transition... |
| rcombinator | rcombinator: A package for simulating evolution of genetic... |
| recombine_sequences | Takes two sequences and returns a recombination of the two... |
| retrotransposon_evolution | Simulates the evolution of a family of sequences by taking... |
| simulate_burst_evolution | Simulates the evolution of a family of sequences by taking... |
| simulate_bursts | Simulate the increase in copy numbers of sequences |
| simulate_point_mutation_markov | The Markov chain simulation for point mutations on a list of... |
| simulate_point_mutation_markov_cheap | The Markov chain simulation for point mutations on a list of... |
| simulate_point_mutation_markov_expensive | The Markov chain simulation for point mutations on a list of... |
| simulate_recombination | Simulates the evolution of a family of sequences by taking... |
| simulate_recombination_cheap | Simulates the evolution of a family of sequences by taking... |
| simulate_recombination_expensive | Simulates the evolution of a family of sequences by taking... |
| simulate_recombination_families | Simulates the evolution of a family of sequences by taking... |
| simulate_recombination_summary | Simulates the evolution of a family of sequences by taking... |
| simulate_without_recombination | Simulates the evolution of a family of sequences by taking... |
| simulate_without_recombination_cheap | Simulates the evolution of a family of sequences by taking... |
| simulate_without_recombination_expensive | Simulates the evolution of a family of sequences by taking... |
| simulate_without_recombination_families | Simulates the evolution of a family of sequences by taking... |
| simulate_without_recombination_summary | Simulates the evolution of a family of sequences by taking... |
| stringdist_ape | To find the scores between strings using ape distance |
| stringdist_biostrings | To find the scores between strings using Biostrings scores |
| stringdist_levenshtein | To find the scores between strings using Levenshtein distance |
| test_event | Determine whether or not an event will take place |
| update_burst_mean | Updates the mean for the Poisson distribution after a burst... |
| valid_ranges | Checks whether a list of ranges partitions an entire sequence |
