library(wiritttea)
options(warn = 1)
args <- commandArgs(trailingOnly = TRUE)
if (1 == 2) {
args <- c("/home/richel/wirittte_data", "stub")
args <- c("/home/richel/wirittte_data", "20171009")
}
if (length(args) < 1) {
stop("Please add the source superfolder as a first argument, e.g. '~/wirittte_data'")
}
if (length(args) < 2) {
stop("Please add the date as a second argument, e.g. '20170711'")
}
if (length(args) != 2) {
stop("Supply two parameters: a source superfolder and a source subfolder, ",
"e.g. '~/wirittte_data/stub 20170711'")
}
source_superfolder <- args[1]
date <- args[2]
# Variable initialization
print(paste0("source_superfolder: ", source_superfolder))
print(paste0("date: ", date))
# Checking inputs
if (dir.exists(source_superfolder)) {
print("OK: source super folder is a folder")
} else {
stop("ERROR: source super folder is not a folder")
}
# Checking if all files exist
nltt_stats_filename <- paste0(source_superfolder, "/nltt_stats_", date, ".csv")
parameters_filename <- paste0(source_superfolder, "/parameters_", date, ".csv")
alignments_filename <- paste0(source_superfolder, "/alignments_", date, ".csv")
operators_filename <- paste0(source_superfolder, "/operators_", date, ".csv")
esses_filename <- paste0(source_superfolder, "/esses_", date, ".csv")
if (!file.exists(parameters_filename)) {
stop(
"File '", parameters_filename, "' not found, ",
"please run collect_parameters"
)
}
if (!file.exists(nltt_stats_filename)) {
stop("File '", nltt_stats_filename, "' not found, ",
"please run collect_nltt_stats")
}
if (!file.exists(alignments_filename)) {
stop("File '", alignments_filename, "' not found, ",
"please run collect_alignments")
}
if (!file.exists(operators_filename)) {
stop("File '", operators_filename, "' not found, ",
"please run collect_operators")
}
if (!file.exists(esses_filename)) {
stop("File '", esses_filename, "' not found, ",
"please run collect_esses")
}
print("Reading files")
parameters <- wiritttea::read_collected_parameters(parameters_filename)
nltt_stats <- wiritttea::read_collected_nltt_stats(nltt_stats_filename, burn_in_fraction = 0.2)
operators <- wiritttea::read_collected_operators(operators_filename)
alignments <- wiritttea::read_collected_alignments(alignments_filename)
esses <- wiritttea::read_collected_esses(esses_filename)
print("Create figures")
print("create_figure_error")
wiritttea::create_figure_error(
parameters = parameters,
nltt_stats = nltt_stats,
filename = paste0(source_superfolder, "/figure_error_", date, ".svg")
)
print("create_figure_acceptance_mcmc_operators")
wiritttea::create_figure_acceptance_mcmc_operators(
operators = operators,
filename = paste0(source_superfolder, "/figure_acceptance_mcmc_operators_", date, ".svg")
)
print("create_figure_alignment_qualities")
wiritttea::create_figure_alignment_qualities(
alignments = alignments,
filename = paste0(source_superfolder, "/figure_alignment_qualities_", date, ".svg")
)
print("create_figure_error_alignment_length_mean")
wiritttea::create_figure_error_alignment_length_mean(
parameters = parameters,
nltt_stats = nltt_stats,
esses = esses,
filename = paste0(source_superfolder, "/figure_error_alignment_length_", date, ".svg")
)
print("create_figure_error_alignment_length_mean")
wiritttea::create_figure_error_alignment_length_mean(
parameters = parameters,
nltt_stats = nltt_stats,
esses = esses,
filename = paste0(source_superfolder, "/figure_error_alignment_length_mean_", date, ".svg")
)
print("create_figure_error_alignment_length_median")
wiritttea::create_figure_error_alignment_length_median(
parameters = parameters,
nltt_stats = nltt_stats,
esses = esses,
filename = paste0(source_superfolder, "/figure_error_alignment_length_median_", date, ".svg")
)
print("Done")
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