render documentation

R/internal_functions.R

@@ -398,6 +398,10 @@ check_arguments <- function(fun, args){
  checkmate::assert_numeric(x = args$threshold, any.missing = FALSE, all.missing = FALSE, unique = TRUE, lower = 0.0001, upper = 0.999, add = check_collection, .var.name = "threshold")
  }
 
+
+ if (any(names(args) == "peak.amplitude"))
+ checkmate::assert_numeric(x = args$peak.amplitude, any.missing = FALSE, all.missing = FALSE, unique = TRUE, lower = 0, add = check_collection, .var.name = "peak.amplitude")
+
  if (any(names(args) == "thinning"))
  checkmate::assert_numeric(x = args$thinning, any.missing = FALSE, all.missing = FALSE, unique = TRUE, lower = 0.0001, upper = 1, add = check_collection, .var.name = "thinning")
 
@@ -802,22 +806,22 @@ detect_FUN <-
  }
 
  # remove sound events based on duration
- if (min.duration > 0) {
- detections_df <- detections_df[detections_df$duration > min.duration / 1000, ]
+ if (min.dur > 0) {
+ detections_df <- detections_df[detections_df$duration > min.dur / 1000, ]
  }
- if (max.duration < Inf) {
- detections_df <- detections_df[detections_df$duration < max.duration / 1000, ]
+ if (max.dur < Inf) {
+ detections_df <- detections_df[detections_df$duration < max.dur / 1000, ]
  }
  }
 
  # remove extra column
  detections_df$ovlp.sels <- NULL
 
  # measure peak.amplitude
- if (peak.amplitude > 0) {
+ if (pa > 0) {
  detections_df <- warbleR::sound_pressure_level(detections_df, parallel = 1, path = pth, pb = FALSE, type = "peak")
 
- detections_df <- detections_df[detections_df$SPL > peak.amplitude, ]
+ detections_df <- detections_df[detections_df$SPL > pa, ]
 
  # remove extra column
  detections_df$SPL <- NULL

tests/testthat/test-energy_detector.R

@@ -22,7 +22,7 @@ test_that("peak amplitude works", {
  )
  expect_class(detec1, "data.frame")
  expect_class(detec1, "selection_table")
- expect_equal(nrow(detec1), 17)
+ expect_equal(nrow(detec1), 12)
 })
 
 test_that("time diagnostics", {
@@ -42,7 +42,7 @@ test_that("time diagnostics", {
 
  expect_class(detec1, "data.frame")
  expect_class(detec1, "selection_table")
- expect_equal(nrow(detec1), 17)
+ expect_equal(nrow(detec1), 3)
 
 })
 
@@ -59,7 +59,7 @@ test_that("using smoothing and minimum duration", {
  )
  expect_class(detec1, "data.frame")
  expect_class(detec1, "selection_table")
- expect_equal(nrow(detec1), 14)
+ expect_equal(nrow(detec1), 9)
 
 })
 
@@ -80,8 +80,6 @@ test_that("using hold time", {
 
 })
 
-
-
 test_that("calculate envelopes first", {
  envs <- get_envelopes(
  files = c("lbh1.wav", "lbh2.wav"),