# R/sensi_plot.tree.bd.R In sensiPhy: Sensitivity Analysis for Comparative Methods

#### Documented in sensi_plot.tree.bd

```#' Graphical diagnostics for class 'tree.physig'
#'
#' \code{sensi_plot_tree.bd} Plot results from \code{tree_bd}.
#' @param x output from \code{tree_bd}
#' @param graphs choose which graph should be printed in the output ("all", 1 or 2)
#' @param ... further arguments to methods
#' @importFrom ggplot2 scale_color_manual geom_histogram geom_abline geom_density
#' geom_vline xlab geom_point theme
#' @author Caterina Penone and Gustavo Paterno
#' @details For 'x' from \code{tree_bd}
#'
#' \strong{Graphs 1:} Distribution of estimated diversification or speciation rate
#'  for each tree. Red vertical line represents the average signal among all estimates.
#'
#' \strong{Graphs 2:} Estimates across each phylogenetic tree.
#'
#' @importFrom grid unit
#' @importFrom stats plogis
#' @importFrom stats reorder
#' @export
sensi_plot.tree.bd <- function(x, graphs="all", ...){

### Nulling variables
estimate <- n.tree <- model <- NULL
### Basic checking:
method <- x\$call\$method
if(is.null(x\$call\$method)) method <- "ms"
if (method == "ms") label = "estimated diversification rate [ms]"
if (method == "km") label = "estimated speciation rate [km]"
### Distribution of ms values estimated
e1 <- ggplot2::ggplot(x\$tree.bd.estimates, aes(x=estimate))+
geom_histogram(fill="yellow",colour="black", size=.2,
alpha = .3) +
geom_vline(xintercept = x\$stats\$mean, color="red",linetype=2,size=.7)+
xlab(label)+
ylab("Frequency")+
theme(axis.title=element_text(size=12),
axis.text = element_text(size=12),
panel.background = element_rect(fill="white",
colour="black"))

### Distribution of Values estimated
e2 <- ggplot2::ggplot(x\$tree.bd.estimates,
aes(y = estimate, x = reorder(n.tree, estimate)))+
geom_point(size = 3, color = "tomato") +
xlab("tree")+
ylab("estimate")+
theme(axis.title=element_text(size=12),
axis.text.x = element_text(size=8),
axis.text.y = element_text(size=12),
panel.background = element_rect(fill="white",
colour="black"))
### Plotting:
if (graphs=="all")
suppressMessages(return(multiplot(e1,e2, cols=2)))
if (graphs==1)
suppressMessages(return(e1))
if (graphs==2)
suppressMessages(return(e2))
}
```

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sensiPhy documentation built on April 14, 2020, 7:15 p.m.