data-raw/create_islands.R

In joshwlambert/relaxedDAISIE: Reproduce Relaxed-rate DAISIE Paper

## code to prepare island dataset goes here
## The data sets selected and saved in this script have passed a set of
## criteria to be used in the analysis
## Criterion 1) the island must have at least 6 colonisation events
## Criterion 2) the island must have at least 50% phylogenetic sampling
## Criterion 3) the island must have variation in clade size (i.e.
## some clades have radiated while others have not)

# load data of all 41 islands/archipelagos stored in the DAISIE package
utils::data(archipelagos41, package = "DAISIE")

# loop through all 41 islands and assign them to their own object
for (i in seq_along(archipelagos41)) {
  assign(paste(archipelagos41[[i]][[1]]$name), archipelagos41[[i]])
}

# Canaries

# remove superfluous meta data
Canaries[[1]] <- list(island_age = Canaries[[1]]$island_age, #nolint
                      not_present = Canaries[[1]]$not_present)

# save island data
usethis::use_data(Canaries, overwrite = TRUE)

# Comoros

# remove superfluous meta data
Comoros[[1]] <- list(island_age = Comoros[[1]]$island_age, #nolint
                     not_present = Comoros[[1]]$not_present)

# save island data
usethis::use_data(Comoros, overwrite = TRUE)

# Galapagos

# remove superfluous meta data
Galapagos[[1]] <- list(island_age = Galapagos[[1]]$island_age, #nolint
                       not_present = Galapagos[[1]]$not_present)

# fix typo
Galapagos[[4]]$colonist_name <- "Camarhynchus heliobates" # nolint

# save island data
usethis::use_data(Galapagos, overwrite = TRUE)

# Galapagos 2 type

Galapagos_2type <- Galapagos #nolint
Galapagos_2type[[1]] <- list(island_age = Galapagos[[1]]$island_age, #nolint
                             not_present_type1 = 830,
                             not_present_type2 = 162)
Galapagos_2type[[4]]$type1or2 <- 2 #nolint

# save island data
usethis::use_data(Galapagos_2type, overwrite = TRUE)


# Hawaii

# remove superfluous meta data
Hawaii[[1]] <- list(island_age = Hawaii[[1]]$island_age, #nolint
                    not_present = Hawaii[[1]]$not_present)

# save island data
usethis::use_data(Hawaii, overwrite = TRUE)

# Hawaii 2 type

Hawaii_2type <- Hawaii #nolint
Hawaii_2type[[1]] <- list(island_age = Hawaii[[1]]$island_age, #nolint
                          not_present_type1 = 793,
                          not_present_type2 = 199)
Hawaii_2type[[3]]$type1or2 <- 2 #nolint

# save island data
usethis::use_data(Hawaii_2type, overwrite = TRUE)

# Marquesas

# remove superfluous meta data
Marquesas[[1]] <- list(island_age = Marquesas[[1]]$island_age, #nolint
                       not_present = Marquesas[[1]]$not_present)

# save island data
usethis::use_data(Marquesas, overwrite = TRUE)

# Marquesas 2 type

Marquesas_2type <- Marquesas #nolint
Marquesas_2type[[1]] <- list(island_age = Marquesas[[1]]$island_age, #nolint
                             not_present_type1 = 887,
                             not_present_type2 = 99)
Marquesas_2type[[2]]$type1or2 <- 2 #nolint

# save island data
usethis::use_data(Marquesas_2type, overwrite = TRUE)

# New Caledonia

# remove superfluous meta data
New_Caledonia[[1]] <- list(island_age = New_Caledonia[[1]]$island_age, #nolint
                           not_present = New_Caledonia[[1]]$not_present)

# save island data
usethis::use_data(New_Caledonia, overwrite = TRUE)


# Sao Tome and Principe

# remove superfluous meta data
SaoTome_Principe[[1]] <- list(island_age = SaoTome_Principe[[1]]$island_age, #nolint
                              not_present = SaoTome_Principe[[1]]$not_present)

# save island data
usethis::use_data(SaoTome_Principe, overwrite = TRUE)