Description Usage Arguments Value Examples
A function to plot a scatterplot of (model-averaged) diversification rates in the alternative states. We can change the rate plotted on the y axis and modify the label for the x-axis (your binary 0/1 trait).
1 2 3 4 5 6 7 | h_scatterplot(
processed_recon,
parameter = "turnover",
states_names = c("0", "1"),
colors = c("yellow", "violet"),
plot_as_waiting_time = FALSE
)
|
processed_recon |
An object produced by |
parameter |
The diversification parameter to be plotted on the y axis. Possible options are turnover, extinct.frac, net.div, speciation, extinction |
states_names |
A character vector of length two giving the translation for states 0 and 1 |
colors |
Colors for the points in the two alternate states |
plot_as_waiting_time |
Logical. Whether to plot the rates or their inverse (waiting times) |
A jittered scatterplot of (model averaged) tip-associated rates.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 | data("diatoms")
processed_hisse <- h_process_recon(hisse_recon=diatoms$cid4_recon)
hisse_rates_plot <- h_scatterplot(
processed_recon=processed_hisse,
parameter="turnover")
# modifications are easy with ggplot
# change x axis tick labels
hisse_rates_plot +
scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos"))
# change the position of the legend
hisse_rates_plot +
scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos")) +
theme(legend.position="top")
# use expressions (for greek letters) in the axis labels
hisse_rates_plot +
scale_x_discrete(breaks=c(0,1), labels=c("plankton", "benthos")) +
theme(legend.position="top") +
labs(y=expression(paste(tau, "=", lambda, "+", mu))) +
theme(axis.text.y=element_text(size=15))
|
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