detectNLP {soundgen}

Detect NLP

Description

(Experimental) A function for automatically detecting and annotating nonlinear vocal phenomena (NLP). Algorithm: analyze the audio using analyze and phasegram, then use the extracted frame-by-frame descriptives to classify each frame as having no NLP ("none"), subharmonics ("sh"), sibebands / amplitude modulation ("sb"), or deterministic chaos ("chaos"). The classification is performed by a naiveBayes algorithm adapted to autocorrelated time series and pretrained on a manually annotated corpus of vocalizations. Whenever possible, check and correct pitch tracks prior to running the algorithm. See naiveBayes for tips on using adaptive priors and "clumpering" to account for the fact that NLP typically occur in continuous segments spanning multiple frames.

Usage

detectNLP(
  x,
  samplingRate = NULL,
  predictors = c("nPeaks", "d2", "subDep", "amEnvDep", "entropy", "HNR", "CPP",
    "roughness"),
  thresProb = 0.4,
  unvoicedToNone = FALSE,
  train = soundgen::detectNLP_training_nonv,
  scale = NULL,
  from = NULL,
  to = NULL,
  pitchManual = NULL,
  pars_analyze = list(windowLength = 50, roughness = list(windowLength = 15, step = 3)),
  pars_phasegram = list(nonlinStats = "d2"),
  pars_naiveBayes = list(prior = "static", wlClumper = 3),
  jumpThres = 14,
  jumpWindow = 100,
  reportEvery = NULL,
  cores = 1,
  plot = FALSE,
  savePlots = NULL,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  ylim = NULL,
  width = 900,
  height = 500,
  units = "px",
  res = NA,
  ...
)

Arguments

x

path to a folder, one or more wav or mp3 files c('file1.wav', 'file2.mp3'), Wave object, numeric vector, or a list of Wave objects or numeric vectors

samplingRate

sampling rate of x (only needed if x is a numeric vector)

predictors

variables to include in NLP classification. The default is to include all 7 variables in the training corpus. NA values are fine (they do not cause the entire frame to be dropped as long as at least one variable is measured).

thresProb

minimum probability of NLP for the frame to be classified as non-"none", which is good for reducing false alarms (<1/nClasses means just go for the highest probability)

unvoicedToNone

if TRUE, frames treated as unvoiced are set to "none" (mostly makes sense with manual pitch tracking)

train

training corpus, namely the result of running naiveBayes_train on audio with known NLP episodes. Currently implemented: soundgen::detectNLP_training_nonv = manually annotated human nonverbal vocalizations, soundgen::detectNLP_training_synth = synthetic, soundgen()-generated sounds with various NLP. To train your own, run detectNLP on a collection of recordings, provide ground truth classification of NLP per frame (normally this would be converted from NLP annotations), and run naiveBayes_train.

scale

maximum possible amplitude of input used for normalization of input vector (only needed if x is a numeric vector)

from, to

if NULL (default), analyzes the whole sound, otherwise from...to (s)

pitchManual

manually corrected pitch contour. For a single sound, provide a numeric vector of any length. For multiple sounds, provide a dataframe with columns "file" and "pitch" (or path to a csv file) as returned by pitch_app, ideally with the same windowLength and step as in current call to analyze. A named list with pitch vectors per file is also OK (eg as returned by pitch_app)

pars_analyze

arguments passed to analyze. NB: drop everything unnecessary to speed up the process, e.g. nFormants = 0, loudness = NULL, etc. If you have manual pitch contours, pass them as pitchManual = .... Make sure the "silence" threshold is appropriate, and ideally normalize the audio (silent frames are automatically assigned to "none")

pars_phasegram

arguments passed to phasegram. NB: only d2 and nPeaks are used for NLP detection because they proved effective in the training corpus; other nonlinear statistics are not calculated to save time.

pars_naiveBayes

arguments passed to naiveBayes. It is strongly recommended to use some clumpering, with wlClumper given as frames (multiple by step to get the corresponding minumum duration of an NLP segment in ms), and/or dynamic priors.

jumpThres

frames in which pitch changes by jumpThres octaves/s more than in the surrounding frames are classified as containing "pitch jumps". Note that this is the rate of frequency change PER SECOND, not from one frame to the next

jumpWindow

the window for calculating the median pitch slope around the analyzed frame, ms

reportEvery

when processing multiple inputs, report estimated time left every ... iterations (NULL = default, NA = don't report)

cores

number of cores for parallel processing

plot

if TRUE, produces a spectrogram with annotated NLP regimes

savePlots

full path to the folder in which to save the plots (NULL = don't save, ” = same folder as audio)

main, xlab, ylab, ...

graphical parameters passed to spectrogram

ylim

frequency range to plot, kHz (defaults to 0 to Nyquist frequency). NB: still in kHz, even if yScale = bark, mel, or ERB

width, height, units, res

parameters passed to png if the plot is saved

Value

Returns a dataframe with frame-by-frame descriptives, posterior probabilities of each NLP type per frame, and the tentative classification (the NLP type with the highest posterior probability, possibly corrected by clumpering). The time step is equal to the larger of the steps passed to analyze() and phasegram().

Returns a list of datasets, one per input file, with acoustic descriptives per frame (returned by analyze and phasegram), probabilities of each NLP type per frame, and the putative classification of NLP per frame.

Examples

## Not run: 
target = soundgen(sylLen = 1600, addSilence = 0, temperature = 1e-6,
  pitch = c(380, 550, 500, 220), subDep = c(0, 0, 40, 0, 0, 0, 0, 0),
  amDep = c(0, 0, 0, 0, 80, 0, 0, 0), amFreq = 80,
  noise = c(-10, rep(-40, 5)),
  jitterDep = c(0, 0, 0, 0, 0, 3))

# classifier trained on manually annotated recordings of human nonverbal
# vocalizations
nlp = detectNLP(target, 16000, plot = TRUE, ylim = c(0, 4))

# classifier trained on synthetic, soundgen()-generated sounds
nlp = detectNLP(target, 16000, train = soundgen::detectNLP_training_synth,
                plot = TRUE, ylim = c(0, 4))
head(nlp[, c('time', 'pr')])
table(nlp$pr)
plot(nlp$amEnvDep, type = 'l')
plot(nlp$subDep, type = 'l')
plot(nlp$entropy, type = 'l')
plot(nlp$none, type = 'l')
points(nlp$sb, type = 'l', col = 'blue')
points(nlp$sh, type = 'l', col = 'green')
points(nlp$chaos, type = 'l', col = 'red')

# detection of pitch jumps
s1 = soundgen(sylLen = 1200, temperature = .001, pitch = list(
  time = c(0, 350, 351, 890, 891, 1200),
  value = c(140, 230, 460, 330, 220, 200)))
playme(s1, 16000)
detectNLP(s1, 16000, plot = TRUE, ylim = c(0, 3))

# process all files in a folder
nlp = detectNLP('/home/allgoodguys/Downloads/temp260/',
  pitchManual = soundgen::pitchContour, cores = 4, plot = TRUE,
  savePlots = '', ylim = c(0, 3))

## End(Not run)