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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