Nothing
## ---- include = FALSE---------------------------------------------------------
library(nLTT) #nolint
require(ggplot2)
require(knitr)
# temporary fix to keep R-devel happy.
# should be updated upon release of version 3.6
suppressWarnings(RNGversion("3.5.0"))
## -----------------------------------------------------------------------------
newick1 <- "((A:1,B:1):2,C:3);"
newick2 <- "((A:2,B:2):1,C:3);"
phylogeny1 <- ape::read.tree(text = newick1)
phylogeny2 <- ape::read.tree(text = newick2)
phylogenies <- c(phylogeny1, phylogeny2)
## -----------------------------------------------------------------------------
ape::plot.phylo(phylogeny1)
ape::add.scale.bar() #nolint
## -----------------------------------------------------------------------------
nLTT::nltt_plot(phylogeny1, ylim = c(0, 1))
## -----------------------------------------------------------------------------
t <- nLTT::get_phylogeny_nltt_matrix(phylogeny1)
knitr::kable(t)
## -----------------------------------------------------------------------------
df <- as.data.frame(nLTT::get_phylogeny_nltt_matrix(phylogeny1))
ggplot2::qplot(
time, N, data = df, geom = "step", ylim = c(0, 1), direction = "vh",
main = "NLTT plot of phylogeny 1"
)
## -----------------------------------------------------------------------------
ape::plot.phylo(phylogeny2)
ape::add.scale.bar() #nolint
## -----------------------------------------------------------------------------
nLTT::nltt_plot(phylogeny2, ylim = c(0, 1))
## -----------------------------------------------------------------------------
t <- nLTT::get_phylogeny_nltt_matrix(phylogeny2)
knitr::kable(t)
## -----------------------------------------------------------------------------
df <- as.data.frame(nLTT::get_phylogeny_nltt_matrix(phylogeny2))
ggplot2::qplot(
time, N, data = df, geom = "step", ylim = c(0, 1), direction = "vh",
main = "NLTT plot of phylogeny 2"
)
## -----------------------------------------------------------------------------
t <- nLTT::stretch_nltt_matrix(
nLTT::get_phylogeny_nltt_matrix(phylogeny1), dt = 0.20, step_type = "upper"
)
knitr::kable(t)
## -----------------------------------------------------------------------------
t <- nLTT::stretch_nltt_matrix(
nLTT::get_phylogeny_nltt_matrix(phylogeny2), dt = 0.20, step_type = "upper"
)
knitr::kable(t)
## -----------------------------------------------------------------------------
t <- nLTT::get_average_nltt_matrix(phylogenies, dt = 0.20)
knitr::kable(t)
## -----------------------------------------------------------------------------
nLTT::nltts_plot(phylogenies, dt = 0.20, plot_nltts = TRUE)
## -----------------------------------------------------------------------------
t <- nLTT::get_nltt_values(c(phylogeny1, phylogeny2), dt = 0.2)
knitr::kable(t)
## -----------------------------------------------------------------------------
df <- nLTT::get_nltt_values(c(phylogeny1, phylogeny2), dt = 0.01)
## ----fig.width = 7, fig.height = 7--------------------------------------------
ggplot2::qplot(
t, nltt, data = df, geom = "point", ylim = c(0, 1),
main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)
) + ggplot2::stat_summary(
fun.data = "mean_cl_boot", color = "red", geom = "smooth"
)
## -----------------------------------------------------------------------------
ggplot2::qplot(t, nltt, data = df, geom = "blank", ylim = c(0, 1),
main = "Average nLTT plot of phylogenies"
) + ggplot2::stat_summary(
fun.data = "mean_cl_boot", color = "red", geom = "smooth"
)
## -----------------------------------------------------------------------------
newick1 <- "((A:1,B:1):1,(C:1,D:1):1);"
newick2 <- paste0("((((XD:1,ZD:1):1,CE:2):1,(FE:2,EE:2):1):4,((AE:1,BE:1):1,",
"(WD:1,YD:1):1):5);"
)
phylogeny1 <- ape::read.tree(text = newick1)
phylogeny2 <- ape::read.tree(text = newick2)
phylogenies <- c(phylogeny1, phylogeny2)
## -----------------------------------------------------------------------------
ape::plot.phylo(phylogeny1)
ape::add.scale.bar() #nolint
## -----------------------------------------------------------------------------
nLTT::nltt_plot(phylogeny1, ylim = c(0, 1))
## -----------------------------------------------------------------------------
t <- nLTT::get_phylogeny_nltt_matrix(phylogeny2)
knitr::kable(t)
## -----------------------------------------------------------------------------
ape::plot.phylo(phylogeny2)
ape::add.scale.bar() #nolint
## -----------------------------------------------------------------------------
nLTT::nltt_plot(phylogeny2, ylim = c(0, 1))
## -----------------------------------------------------------------------------
t <- nLTT::get_phylogeny_nltt_matrix(phylogeny2)
knitr::kable(t)
## -----------------------------------------------------------------------------
t <- nLTT::stretch_nltt_matrix(
nLTT::get_phylogeny_nltt_matrix(phylogeny1), dt = 0.20, step_type = "upper"
)
knitr::kable(t)
## -----------------------------------------------------------------------------
t <- nLTT::stretch_nltt_matrix(
nLTT::get_phylogeny_nltt_matrix(phylogeny2), dt = 0.20, step_type = "upper"
)
knitr::kable(t)
## -----------------------------------------------------------------------------
t <- nLTT::get_average_nltt_matrix(phylogenies, dt = 0.20)
knitr::kable(t)
## -----------------------------------------------------------------------------
t <- nLTT::get_nltt_values(c(phylogeny1, phylogeny2), dt = 0.2)
knitr::kable(t)
## -----------------------------------------------------------------------------
df <- nLTT::get_nltt_values(c(phylogeny1, phylogeny2), dt = 0.01)
## ----fig.width = 7, fig.height = 7--------------------------------------------
ggplot2::qplot(
t, nltt, data = df, geom = "point", ylim = c(0, 1),
main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)
) + ggplot2::stat_summary(
fun.data = "mean_cl_boot", color = "red", geom = "smooth"
)
## ----fig.width = 7, fig.height = 7--------------------------------------------
ggplot2::qplot(t, nltt, data = df, geom = "blank", ylim = c(0, 1),
main = "Average nLTT plot of phylogenies"
) + ggplot2::stat_summary(
fun.data = "mean_cl_boot", color = "red", geom = "smooth"
)
## -----------------------------------------------------------------------------
set.seed(42)
phylogeny1 <- ape::rcoal(10)
phylogeny2 <- ape::rcoal(20)
phylogeny3 <- ape::rcoal(30)
phylogeny4 <- ape::rcoal(40)
phylogeny5 <- ape::rcoal(50)
phylogeny6 <- ape::rcoal(60)
phylogeny7 <- ape::rcoal(70)
phylogenies <- c(
phylogeny1, phylogeny2, phylogeny3,
phylogeny4, phylogeny5, phylogeny6, phylogeny7
)
## -----------------------------------------------------------------------------
t <- nLTT::get_nltt_values(phylogenies, dt = 0.2)
knitr::kable(t)
## ----fig.width = 7, fig.height = 7--------------------------------------------
ggplot2::qplot(t, nltt, data = df, geom = "point", ylim = c(0, 1),
main = "Average nLTT plot of phylogenies", color = id, size = I(0.1)
) + ggplot2::stat_summary(
fun.data = "mean_cl_boot", color = "red", geom = "smooth"
)
## ----fig.width = 7, fig.height = 7--------------------------------------------
ggplot2::qplot(t, nltt, data = df, geom = "blank", ylim = c(0, 1),
main = "Average nLTT plot of phylogenies"
) + ggplot2::stat_summary(
fun.data = "mean_cl_boot", color = "red", geom = "smooth"
)
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