nltt_diff.R
In nLTT: Calculate the NLTT Statistic

## ----fig.width=2--------------------------------------------------------------
# normalized number of lineages
#
# 1.0 +   X---X                                            #nolint
#     |   |
# 0.5 X---+                                                #nolint
#     |
#     +---+---+
#        0.5 1.0   normalized time
#
#
#
# normalized number of lineages
#
##  1.0  +       X                                         #nolint
##  0.75 |   X---+
##  0.5  |   |
##  0.25 X---+
##       +---+---+
##         0.5 1.0   normalized time

## -----------------------------------------------------------------------------
phylogeny_1 <- ape::read.tree(text = "(a:1,b:1):1;")
phylogeny_2 <- ape::read.tree(
  text = "(((d:0.000000001,c:0.000000001):1,b:1):0.000000001,a:1.000000001):1;")
ape::plot.phylo(phylogeny_1, root.edge = TRUE)
ape::plot.phylo(phylogeny_2, root.edge = TRUE)

## -----------------------------------------------------------------------------
nLTT::nltt_plot(phylogeny_1, ylim = c(0, 1)); nLTT::nltt_lines(phylogeny_2)

## -----------------------------------------------------------------------------
nltt_stat <- nLTT::nltt_diff(phylogeny_1, phylogeny_2)
nltt_stat_exact <- nLTT::nltt_diff_exact(phylogeny_1, phylogeny_2)
testthat::expect_equal(nltt_stat, 0.25, tolerance = 0.0001)
testthat::expect_equal(nltt_stat_exact, 0.25, tolerance = 0.0001)

## -----------------------------------------------------------------------------
b_times <- nLTT::get_branching_times(phylogeny_1)
lineages <- nLTT::get_n_lineages(phylogeny_1)
b_times2 <- nLTT::get_branching_times(phylogeny_2)
lineages2 <- nLTT::get_n_lineages(phylogeny_2)
df <- data.frame(b_times = b_times, lineages = lineages)
knitr::kable(df)
df2 <- data.frame(b_times2 = b_times2, lineages2 = lineages2)
knitr::kable(df2)

## -----------------------------------------------------------------------------
nltt_stat_exact <- nLTT::nltt_diff_exact_brts(
  b_times = b_times,
  lineages = lineages,
  b_times2 = b_times2,
  lineages2 = lineages2,
  distance_method = "abs",
  time_unit = "ago")

testthat::expect_equal(nltt_stat_exact, 0.25, tolerance = 0.0001)

## -----------------------------------------------------------------------------
b_times_n <- nLTT::get_norm_brts(phylogeny_1)
lineages_n <- nLTT::get_norm_n(phylogeny_1)
b_times2_n <- nLTT::get_norm_brts(phylogeny_2)
lineages2_n <- nLTT::get_norm_n(phylogeny_2)
df <- data.frame(b_times_n = b_times_n, lineages_n = lineages_n)
knitr::kable(df)
df2 <- data.frame(b_times2_n = b_times2_n, lineages2_n = lineages2_n)
knitr::kable(df2)