Build an identification key from PhyloTree Build 17

Turns phylotree17, or the part of it below root, into a dimoose key. Each haplogroup with subclades becomes a step at which the user picks the subclade whose defining mutations the sample carries. With paragroups = TRUE every step also offers "none of these", which identifies the paragroup, written as in PhyloTree with a trailing * (e.g. H2a*).

Usage

phylotreeKey(root = "mtMRCA", paragroups = TRUE, maxDepth = Inf)

Arguments

root: Haplogroup to start from; the default, "mtMRCA", is the whole tree.
paragroups: If TRUE, add a "none of these" choice to every step.
maxDepth: Maximum number of steps below root. Haplogroups at that depth become results even if they have subclades.

Value

A dimoose object whose leads have a Label column with the haplogroup names.

Details

The whole tree gives a very large key (2,420 steps and 5,435 possible results with paragroups), so for exportWizard() a subtree or a maxDepth is usually more practical.

Examples

h2a <- phylotreeKey("H2a")
head(h2a$leads)
#>   Statement Choice                   Character Next Taxon Label
#> 1       H2a      1                 951A 16354T H2a1        H2a1
#> 2       H2a      2                        750A H2a2        H2a2
#> 3       H2a      3              10810C! 16274A H2a3        H2a3
#> 4       H2a      4                      11140T    -  H2a4  H2a4
#> 5       H2a      5                      13708A H2a5        H2a5
#> 6       H2a      6 None of the subclades above    -  H2a*  H2a*
if (FALSE) { # \dontrun{
exportWizard(phylotreeKey("U5"), "u5.html")
exportWizard(phylotreeKey(maxDepth = 6), "macrohaplogroups.html")
} # }