Man pages for JacobLemieux/sars2phylo
Functions for analyzing SARS-CoV-2 phylogenetic data
| constructHaploTable | construct a table of haplotypes by month |
| convertMonth | convert month to sequential month (jmonth) and week to... |
| countByInterval | create count of a given lineage by given time interval |
| createSgenoTable | create a table of genotypes in a lineage |
| encodeGenotype | encode genotypes as columns using one-hot encoding |
| encodeLineage | one-hot encoding lineage as binary outcome, as augmented... |
| encodeSgeno | encode S genotype as columns using one-hot encoding |
| extractS | extract S haplotypes from a list of mutations (e.g. called by... |
| logRegFit | fit logistic regression and return coefficients and p values |
| plotCounts | plot absolute counts by timeInt |
| plotLineage | Plot lineage as successes/failures over time, and fit... |
| plotProp | plot proportion by time interval with 95 percent CI |
| plotTop | plot top scoring lineages |
| plotVarWeekly | Create plotting function for lineage with x bins as week, not... |
| plotVOC | plot variants of concern (B.1.1.7, B.1.351, P.1) |
| plotWeekly | plot lineages as successes by week (for accurate uncertainty... |
| readNextClade | read and parse nextclade results |
| readSampleSet | read sample set |
| readTerra | read terra assemblies tsv |
| relabel_DNAss | relabel sequences for BEAST |
