| buildNetwork | Generating a list for construction a network using the... |
| countPanGenes | Counting genes in a pangenome when randomly sampling a series... |
| cumuCurve | Calculating cumulative proportions of objects in a sample... |
| df2matrix | Coverts a dataframe that corresponds to either the... |
| distsPerClade | Summarising phylogenetic distances for each clade in a rooted... |
| epiLinksPatientIsolates | Identifying epidemiological links with isolates from a... |
| estimateCollectionDates | Estimating dates of sample collection |
| getBinaryCoefficient | Calculate association or similarity coefficient for two... |
| getMRCAdates | Getting the date of the most-recent common ancestor (MRCA)... |
| labelGenerator | Creating labels for an axis at a given interval so that ticks... |
| makeFastANIDistMatrix | Make a distance matrix from FastANI output (tab-delimited... |
| makeNamedList | Returns a one- or two-dimensional list with names for each... |
| maskMatrix | Generating a matrix consisting of 0/1 for filtering values in... |
| matrix2df | Coverting the upper triangle of a symmetric numeric matrix... |
| matrixCutoff | Resets a value in an input matrix if it is smaller/greater... |
| maxDaysBetweenDateRanges | Calculating maximum days between collection dates of isolates |
| maxRange | Obtain the maximum range comprising two numeric vectors v1... |
| mkContingencyTable | Making a contingency table from four entries |
| phiCoe | Calculating a phi association coefficient from two binary... |
| plotCI | Plotting 95-percent confidence interval and dated tree in the... |
| plotFishersP | Simulating and plotting probabilities in a Fisher's exact... |
| plotGeneAccumulationCurves | Drawing gene-accumulation curves for a pangenome |
| plotMetaTree | Drawing a metatree (i.e. tree + data + metadata) to either... |
| rmSubclades | Removing IDs of sub-clades from a vector of clade names... |
| scatterPlot | Making a scatter plot of x against y, colour coded by z. |
| seqDepth | Calculating sequencing depths from the output of 'seqkit... |
| simCoe | Simpson's similarity coefficient between two binary vectors |
| sm | Show a diagonal matrix m[start : end, start : end]. |
| splitVec | Splitting a vector into a list of n vectors |
| subsetDfCon | Taking a subset of a data frame in accordance with one or... |
| summariseSeqkitPEReadStats | Summarising statistics of paired-end read sets |
| tab2df | Table to data frame |
| testIndependency | Testing the independency of two variables according to a... |
| upperTriangleToSquareMatrix | Converting a data frame representing an upper triangle matrix... |
| writePHYLIPmatrix | Create a PHYLIP-formatted distance matrix from the output of... |
