Analysis of transmission and intrahost iSNV data taken as part of the HIVE cohort

accuracy_stringent | Sequencing specificity and sensitivity |

betabin_sim | Simulate transmission Beta binomial model |

betabin_sim_helper | beta bin sim helper |

com_sample_trans | Randomly sample a transmission tibble based on a list of... |

correct_id | Correct numerical Ids In our analysis the Id column refers to... |

dist_prob | Fit a distribution to pair_wise bottlenecks |

dist_prob_wrapper | Make distribution specific functions to fit distribution |

dist_tp | Get the genetic distance between two samples . |

diverse_sites | Get sites with diverisity |

dzpois | PMF of a zero truncated Poisson distribution |

equal_compare | Fair base call comparisons. |

finding_valid | Validating transmission pairs |

get_close | Finding SPECID for transmission pairs |

get_double | Get all ENROLLID that have two SPECID in a season with same... |

get_freqs | Get and compare the frequencies of mutations in two samples. |

getting_tp | Finding transmission pairs |

g_ft | Likelihood of frequency starting at 0 |

is_wholenumber | Is this a whole number |

L.Nb.beta | Betabinomial Likelihood functions |

longform_pairs | Convert short paired data to long paired data. |

math_fit | The probability of lambda for a loci |

model_summary | Summarize model likelihoods |

monomorphic | Set monomorphic sites to freq =1 |

mut_model_LL | Mutation rate and Ne from spectrum |

not_detected | Probability of not detecting a polymorphism This is the... |

only_one | Picking one sample per person |

p0 | Mutational model- non polmorphic |

p_all | Probability of drawing an allele n times in n draws |

pa_sim | Simulate transmission Presence absence model |

pa_sim_helper | PA sim helper |

polish_freq | Polishing compared frequencies. |

quality | Identify quality variants |

read_rbind | Read in a list of files |

rzpois | Randomly sample a zero truncated Poisson |

sample_trans | Randomly sample a transmission data.frame without any... |

short_pairs | Convert long paired data to short paired data. |

sift_dups | Sift duplicate calls Take in a data frame of one mutation... |

simulations | Simulate probability of transmission based on frequency |

small_community.comp | iSNV comparison between samples |

small_isnv | iSNV present in samples |

small_meta | A small meta data file |

small_trans | Transmission pairs iSNV |

split_path | Split a file path at / |

trans_fit | Fit the transmission model |

variants | Variant data |

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