Mean clock rates by node and clade (3 clock partitions)
A data set containing the mean clock rates for a tree with 3 clock partitions, such as the output of
get_clockrate_table_MrBayes but with an additional "clade" column added, which is required for use in
A data frame with 79 observations on the following 5 variables.
A character vector containing the clade names for each corresponding node
A numeric vector for the node numbers in the summary tree
A numeric vector containing the mean posterior clock rate for each node for the first partition
A numeric vector containing the mean posterior clock rate for each node for the second partition
A numeric vector containing the mean posterior clock rate for each node for the third partition
RateTable_Means_3p_Clades was created by running
get_clockrate_table_MrBayes(tree3p) and then adding a "clade" column. It can be produced by using the following procedure:
1) Import tree file:
2) Produce clock rate table with, for instance, mean rate values from each branch in the tree:
rate_table <- get_clockrate_table_MrBayes(tree3p, summary = "mean")
write.csv(rate_table, file = "rate_table.csv", row.names = FALSE)
3) Now, manually add clades using, e.g., Excel:
3.1) Manually edit rate_table.csv, adding a "clade" column. This introduces customized clade names to individual nodes in the tree.
3.2) Save the edited rate table with a different name to differentiate from the original output (e.g., rate_table_clades_means.csv).
4) Read the file back in:
RateTable_Means_3p_Clades <- read.csv("rate_table_clades_means.csv")
tree3p for the tree from which the clock rates were extracted.
get_clockrate_table_MrBayes for extracting a clock rate table from a tree.
clockrate_reg_plot for examples of using a clockrate table.