ropensci / beautier
Showing 1 of 1 files from the diff.

@@ -56,13 +56,6 @@
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  input_filename,
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  inference_model
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) {
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  # Alignment IDs
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  ids <- beautier::get_alignment_id(
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    input_filename,
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    capitalize_first_char_id =
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      inference_model$beauti_options$capitalize_first_char_id
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  )
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  # Do not be smart yet
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  site_models <- list(inference_model$site_model)
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  clock_models <- list(inference_model$clock_model)
@@ -71,8 +64,6 @@
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  tipdates_filename <- inference_model$tipdates_filename
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  text <- NULL
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  # 1 tracelog
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  filename <- utils::head(ids, n = 1)
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  text <- c(text, "<log idref=\"posterior\"/>") # nolint this is no absolute path
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  text <- c(text, "<log idref=\"likelihood\"/>") # nolint this is no absolute path
@@ -107,8 +98,23 @@
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  top_line <- paste0(
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    "<logger ",
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    "id=\"tracelog\" ",
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    "fileName=\"", filename, ".log\" ",
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    "id=\"tracelog\" "
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  )
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  if (inference_model$mcmc$tracelog$filename != "") {
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    # Alignment IDs
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    ids <- beautier::get_alignment_id(
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      input_filename,
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      capitalize_first_char_id =
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        inference_model$beauti_options$capitalize_first_char_id
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    )
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    filename <- utils::head(ids, n = 1)
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    top_line <- paste0(
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      top_line,
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      "fileName=\"", filename, ".log\" "
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    )
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  }
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  top_line <- paste0(
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    top_line,
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    "logEvery=\"", inference_model$mcmc$tracelog$log_every, "\" ",
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    "model=\"@posterior\""
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  )
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Project Totals (228 files) 99.57%

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