Commit ⋅ ropensci/beautier

Showing 3 of 5 files from the diff.

93.22% 20.00% -3.27%

R/create_beast2_input_loggers.R changed.

100.00% ø ø

R/create_tracelog.R changed.

100.00% 100.00% ø

R/check_tracelog.R changed.

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tests/testthat/test-create_inference_model.R has changed.

man/create_tracelog.Rd has changed.

@@ -100,7 +100,7 @@

    "<logger ",
    "id=\"tracelog\" "
  )
  if (inference_model$mcmc$tracelog$filename != "") {
  if (is.na(inference_model$mcmc$tracelog$filename)) {
    # Alignment IDs
    ids <- beautier::get_alignment_id(
      input_filename,

@@ -112,6 +112,12 @@

      top_line,
      "fileName=\"", filename, ".log\" "
    )
  } else {
    testit::assert(!is.na(inference_model$mcmc$tracelog$filename))
    top_line <- paste0(
      top_line,
      "fileName=\"", inference_model$mcmc$tracelog$filename, "\" "
    )
  }
  top_line <- paste0(
    top_line,

@@ -1,5 +1,8 @@

#' Create a \code{tracelog} object
#' @param filename name of the file to store the posterior traces
#' @param filename
#'   name of the file to store the posterior traces.
#'   Use \link{NA} to use the filename \code{[alignment_id].log},
#'   where \code{alignment_id} is obtained using \link{get_alignment_id}
#' @param log_every number of MCMC states between the logging of that state
#' phylogenies to. By default, this is \code{$(trace).traces}
#' @param mode mode how to log.

@@ -10,7 +13,7 @@

#' Valid values are the ones returned by \link{get_log_sorts}
#' @export
create_tracelog <- function(
  filename = "test_output_0.log",
  filename = NA,
  log_every = 1000,
  mode = "autodetect",
  sanitise_headers = TRUE,

@@ -44,8 +44,10 @@

#' @noRd
check_tracelog_list_element_values <- function(tracelog) {

  assertive::assert_is_character(tracelog$filename)
  assertive::assert_is_a_string(tracelog$filename)
  if (!beautier::is_one_na(tracelog$filename)) {
    assertive::assert_is_character(tracelog$filename)
    assertive::assert_is_a_string(tracelog$filename)
  }
  assertive::assert_is_numeric(tracelog$log_every)
  assertive::assert_all_are_positive(tracelog$log_every)
  beautier::check_log_mode(tracelog$mode)

Files		•	•	•	Coverage
R	4,619	4,595	0	24	99.48%
Project Totals (228 files)	4,619	4,595	0	24	99.48%

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100	100		"<logger ",
101	101		"id=\"tracelog\" "
102	102		)
103		-	if (inference_model$mcmc$tracelog$filename != "") {
	103	+	if (is.na(inference_model$mcmc$tracelog$filename)) {
104	104		# Alignment IDs
105	105		ids <- beautier::get_alignment_id(
106	106		input_filename,

112	112		top_line,
113	113		"fileName=\"", filename, ".log\" "
114	114		)
	115	+	} else {
	116	+	testit::assert(!is.na(inference_model$mcmc$tracelog$filename))
	117	+	top_line <- paste0(
	118	+	top_line,
	119	+	"fileName=\"", inference_model$mcmc$tracelog$filename, "\" "
	120	+	)
115	121		}
116	122		top_line <- paste0(
117	123		top_line,

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1	1		#' Create a \code{tracelog} object
2		-	#' @param filename name of the file to store the posterior traces
	2	+	#' @param filename
	3	+	#' name of the file to store the posterior traces.
	4	+	#' Use \link{NA} to use the filename \code{[alignment_id].log},
	5	+	#' where \code{alignment_id} is obtained using \link{get_alignment_id}
3	6		#' @param log_every number of MCMC states between the logging of that state
4	7		#' phylogenies to. By default, this is \code{$(trace).traces}
5	8		#' @param mode mode how to log.

10	13		#' Valid values are the ones returned by \link{get_log_sorts}
11	14		#' @export
12	15		create_tracelog <- function(
13		-	filename = "test_output_0.log",
	16	+	filename = NA,
14	17		log_every = 1000,
15	18		mode = "autodetect",
16	19		sanitise_headers = TRUE,

44	44		#' @noRd
45	45		check_tracelog_list_element_values <- function(tracelog) {
46	46
47		-	assertive::assert_is_character(tracelog$filename)
48		-	assertive::assert_is_a_string(tracelog$filename)
	47	+	if (!beautier::is_one_na(tracelog$filename)) {
	48	+	assertive::assert_is_character(tracelog$filename)
	49	+	assertive::assert_is_a_string(tracelog$filename)
	50	+	}
49	51		assertive::assert_is_numeric(tracelog$log_every)
50	52		assertive::assert_all_are_positive(tracelog$log_every)
51	53		beautier::check_log_mode(tracelog$mode)

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