## ----setup, include = FALSE----------------------------------------------
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>"
)
## ----loading_beautier----------------------------------------------------
library(beautier)
## ----is_beast2_input_file_safe-------------------------------------------
is_beast2_input_file_safe <- function(beast2_input_filename) {
tryCatch(
return(beautier:::is_beast2_input_file(beast2_input_filename)),
error = function(cond) {
print("BEAST2 not found")
}
)
TRUE
}
## ----fix-----------------------------------------------------------------
fasta_filename <- get_fasta_filename()
create_beast2_input_file_1_12(
input_filenames = fasta_filename,
output_filename = "fix.xml",
fixed_crown_ages = TRUE,
initial_phylogenies = fasta_to_phylo(
fasta_filename = fasta_filename,
crown_age = 15
)
)
testit::assert(is_beast2_input_file_safe("fix.xml"))
## ----fix_fix-------------------------------------------------------------
fasta_filenames <- get_beautier_paths(c("anthus_aco.fas", "anthus_nd2.fas"))
create_beast2_input_file_1_12(
input_filenames = fasta_filenames,
output_filename = "fix_fix.xml",
fixed_crown_ages = c(TRUE, TRUE),
initial_phylogenies = fastas_to_phylos(
fasta_filename = fasta_filenames,
crown_age = 15
)
)
testit::assert(is_beast2_input_file_safe("fix_fix.xml"))
## ----combinations--------------------------------------------------------
combinations <- list()
combinations[[1]] <- c(FALSE, FALSE)
combinations[[2]] <- c(TRUE, FALSE)
combinations[[3]] <- c(FALSE, TRUE)
for (i in seq_along(combinations)) {
combination <- combinations[[i]]
output_filename <- paste0("combination_", i, ".xml")
create_beast2_input_file_1_12(
input_filenames = fasta_filenames,
output_filename = output_filename,
fixed_crown_ages = combination,
initial_phylogenies = fastas_to_phylos(
fasta_filename = fasta_filenames,
crown_age = 15
)
)
testit::assert(is_beast2_input_file_safe(output_filename))
}
## ----12_34---------------------------------------------------------------
fasta_filenames <- get_beautier_paths(c("anthus_aco.fas", "anthus_nd2.fas"))
initial_phylogenies <- list()
initial_phylogenies[[1]] <- fasta_to_phylo(fasta_filenames[1], crown_age = 12)
initial_phylogenies[[2]] <- fasta_to_phylo(fasta_filenames[2], crown_age = 34)
create_beast2_input_file_1_12(
input_filenames = fasta_filenames,
output_filename = "12_34.xml",
fixed_crown_ages = c(TRUE, TRUE),
initial_phylogenies = initial_phylogenies
)
testit::assert(is_beast2_input_file_safe("12_34.xml"))
## ----cleanup, include = FALSE--------------------------------------------
# Cleaning up
filenames <- c(
"fix.xml",
"fix_fix.xml",
paste0("combination_", seq(1, 3), ".xml"),
"12_34.xml"
)
for (filename in filenames) {
if (file.exists(filename)) file.remove(filename)
}
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