In vtorda/CompareTools: Post processing of COMPARE analysis

knitr::opts_chunk$set(echo = TRUE)

library(ape)
library(plyr)
library(tidyr)
library(stringr)
library(readr)
library(profvis)
library(microbenchmark)

file_path <- system.file("extdata", "Dolloout", package = "CompareTools")
files <- file_path
tree_path <- system.file("extdata", "71g_species.tree", package = "CompareTools")
tree <- read.tree(tree_path)
group_path <- system.file("extdata", "groups.txt", package = "CompareTools")
groups <- group_path
Compare <- DolloImport2(tree = tree, partitioning = FALSE, files = files, part_name = "every")
Compare <- retrieve_event2(Compare, partitioning = TRUE, groups = groups, part_name = "grouped")

which(names(Compare) %in% "every")

class(unlist(Compare$every))
typeof(unlist(Compare$every))
inherits(Compare$every$all_cluster, "numeric")
is.matrix(Compare[[2]][[1]])
as.data.frame(Compare[[2]][[1]])
set <- c("b", "b", "c")
is.character(set)

d <- Compare[[3]][1:1]
raw <- Compare$raw_data
length(Compare[[2]])

PlotEvent(compare = Compare, anlys = "every", set = 1, stat = "cum_gains", sizemeth = "standard")

vtorda/CompareTools documentation built on Nov. 6, 2019, 9:07 p.m.