dispRity: Measuring Disparity

# # #Developer function for making the disparity data
# make.demo.data_BeckLeeXXX <- function() {

#     file.remove("../data/BeckLee_tree.rda")
#     file.remove("../data/BeckLee_ages.rda")
#     file.remove("../data/BeckLee_mat50.rda")
#     file.remove("../data/BeckLee_mat99.rda")

#     set.seed(1)
#     library(dispRity)
#     library(paleotree)
#     library(geiger)
#     source("../tests/testthat/make.data/multi.ace_internal.R")
#     source("../tests/testthat/make.data/convert.tokens.R")
#     source("../tests/testthat/make.data/read.nexus.data.R")
#     ## matrix
#     matrix <- do.call(rbind, read.nexus.data("../tests/testthat/make.data/2014-Beck-ProcB-matrix-morpho.nex"))
#     ## Remove invariant characters
#     matrix <- matrix[, -c(28, 47, 50, 74, 81, 92, 103, 141, 142, 154, 155, 158, 159, 220, 231, 232, 237, 250, 255, 272, 276, 283, 284, 362, 363, 377, 380, 400, 417, 420, 421)]

#     ## tree
#     tree <- read.nexus("../tests/testthat/make.data/2014-Beck-ProcB-TEM.tre")
#     tree_tmp <- extract.clade(tree, 133)
#     tree_tmp <- drop.tip(tree_tmp, extract.clade(tree_tmp, 127)$tip.label)
#     tree <- drop.tip(tree_tmp, c("Erinaceus", "Ptilocercus", "Orycteropus", "Microgale"))
#     tree$node.labels <- paste0("n", seq(1:Nnode(tree)))
#     tree$root.time <- max(tree.age(tree)$age)

#     ## Clean the data
#     cleaned_data <- clean.data(matrix, tree)
#     matrix <- cleaned_data$data
#     tree <- cleaned_data$tree

#     ## Get the FADLADs
#     FADLAD <- read.csv("../tests/testthat/make.data/Beck2014_FADLAD.csv", row.names = 1)
#     FADLAD <- FADLAD[-which(is.na(match(rownames(FADLAD), tree$tip.label))),]

#     ## Add the ancestral states estimates
#     ancestral_states <- multi.ace_internal(matrix, tree, models = "ER", verbose = TRUE)[[1]]
#     rownames(ancestral_states) <- tree$node.labels

#     ## Combine both
#     matrix_tips <- matrix
#     matrix_tips_nodes <- rbind(matrix, ancestral_states)

#     ## Measuring the distance
#     distance_matrix_tips_nodes <- char.diff(matrix_tips_nodes, by.col = FALSE)
#     distance_matrix_tips <- char.diff(matrix_tips, by.col = FALSE)

#     ## Ordination (just because)
#     pco_tips <- cmdscale(distance_matrix_tips, k = nrow(distance_matrix_tips) - 2, add = TRUE)$points
#     pco_tips_nodes <- cmdscale(distance_matrix_tips_nodes, k = nrow(distance_matrix_tips_nodes) - 2, add = TRUE)$points

#     BeckLee_tree <- tree
#     BeckLee_ages <- FADLAD
#     BeckLee_mat50 <- pco_tips
#     BeckLee_mat99 <- pco_tips_nodes

#     ## save the data
#     save(BeckLee_ages, file = "../data/BeckLee_ages.rda")
#     save(BeckLee_tree, file = "../data/BeckLee_tree.rda")
#     save(BeckLee_mat50, file = "../data/BeckLee_mat50.rda")
#     save(BeckLee_mat99, file = "../data/BeckLee_mat99.rda")
# }

# # Developer function for making the disparity data
# make.demo.data_disparity <- function() {
#     file.remove("../data/disparity.rda")
#     set.seed(1)
#     ## Getting the data ready
#     data(BeckLee_tree) ; data(BeckLee_mat99) ; data(BeckLee_ages)

#     ## Creating the time subsets
#     time_subsets <- chrono.subsets(data = BeckLee_mat99, tree = BeckLee_tree, method = "continuous", model = "acctran", time = c(90, 80, 70, 60, 50, 40, 30), FADLAD = BeckLee_ages)

#     ## Bootstrapping the subsets
#     bs_subsets <- boot.matrix(chrono.subsets(data = BeckLee_mat99, tree = BeckLee_tree, method = "continuous", model = "acctran", time = c(90, 80, 70, 60, 50, 40, 30), FADLAD = BeckLee_ages), bootstraps = 100, rarefaction = c(20,15,10,5))

#     ## Calculating disparity
#     disparity <- dispRity(bs_subsets, metric = c(median, centroids))

#     ## save the data
#     save(disparity, file = "../data/disparity.rda")
# }

# # Developer function for making the disparity data
# make.demo.data_BeckLee_disparity <- function() {
#     file.remove("../data/BeckLee_disparity.rda")
#     set.seed(1)
#     ## Getting the data ready
#     data(BeckLee_tree) ; data(BeckLee_mat99) ; data(BeckLee_ages)

#     ## Creating the time subsets
#     time_subsets <- chrono.subsets(data = BeckLee_mat99, tree = BeckLee_tree, method = "continuous", model = "proximity", time = seq(from = 0, to = 120, by = 1), FADLAD = BeckLee_ages)

#     ## Bootstrapping the subsets
#     bs_subsets <- boot.matrix(time_subsets, bootstraps = 100)

#     ## Calculating disparity
#     BeckLee_disparity <- dispRity(bs_subsets, metric = c(sum, variances), verbose = TRUE)

#     ## save the data
#     save(BeckLee_disparity, file = "../data/BeckLee_disparity.rda")
# }

# # make.demo.data_BeckLeeXXX()
# # make.demo.data_disparity()
# # make.demo.data_BeckLee_disparity()