findPeaks: Find Score Peaks and Detections in a 'templateScores' Object
In monitoR: Acoustic Template Detection in R
Description
Usage
Arguments
Details
Value
Author(s)
See Also
Examples
Description
This function accepts templateScores objects and returns information on all score peaks and those peaks that are considered detections.
Usage
1
2
Arguments
score.obj
A templateScores object, produced by corMatch or binMatch.
fd.rat
A ratio of frame width (twice minimum peak separation) to template duration.
frame
If you want the same frame width for templates with varying duration, specify a value directly.
fd.rate will be ignored if frame is specified.
parallel
Set to TRUE for parallel processing using mclapply.
This option is not available for Windows operating systems.
Details
The findPeaks function translates raw scores from template matching to detection information, by finding peaks in the score data, and determining which peaks, if any, exceed the score cutoffs specified in the templates (see the two functions for making templates, makeBinTemplate and makeCorTemplate and templateCutoff for more details on cutoffs).
Value
An S4 object of class templateScores, with the following slots:
survey.name
The file path to the survey that the scores apply to.
survey
The actual survey as a Wave object.
survey.data
A named list with one element per template.
Each element is a named list with time-domain results for the survey.
templates
The templates (an S4 object of class corTemplateList or binTemplateList) used to calculate the scores.
scores
A named list with an element for each template.
Each element contains the scores for an individual template.
peaks
A named list with peak information (as a data frame) for each template.
detections
A named list with detection information (as a data frame) for each template.
Author(s)
Sasha D. Hafner and Jon Katz
See Also
makeCorTemplate,
makeBinTemplate,
corMatch,
binMatch,
getDetections,
getPeaks
Examples
1
2
3
4
5
6
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8
9
10
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14
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17
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19
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63
# Load data
data(btnw)
data(oven)
data(survey)
# Write Wave objects to file (temporary directory used here)
btnw.fp <- file.path(tempdir(), "btnw.wav")
oven.fp <- file.path(tempdir(), "oven.wav")
survey.fp <- file.path(tempdir(), "survey2010-12-31_120000_EST.wav")
writeWave(btnw, btnw.fp)
writeWave(oven, oven.fp)
writeWave(survey, survey.fp)
# Correlation example
# Create two correlation templates
wct <- makeCorTemplate(btnw.fp, t.lim = c(1.5, 2.1), frq.lim = c(4.2, 5.6), name = "w")
oct <- makeCorTemplate(oven.fp, t.lim = c(1, 4), frq.lim = c(1, 11), dens = 0.1, name = "o")
# Combine them
ctemps <- combineCorTemplates(wct, oct)
# Calculate scores
cscores <- corMatch(survey.fp, ctemps)
# Finally, find peaks and detections
cdetects <- findPeaks(cscores)
cdetects
plot(cdetects)
# plotting help:
method?plot('detectionList')
# Binary example
## Not run:
# Not run because of the time required (maybe 2-5 seconds) Create two templates
wbt <- makeBinTemplate(btnw.fp, amp.cutoff = -30, t.lim = c(1.5, 2.1), frq.lim = c(4.2, 5.6),
buffer = 2, name = "w")
obt <- makeBinTemplate(oven.fp, amp.cutoff = -20, t.lim = c(1, 4), frq.lim = c(1, 11),
name = "o")
# Combine them
btemps <- combineBinTemplates(wbt, obt)
# Calculate scores
bscores <- binMatch(survey.fp, btemps)
# Finally, find peaks and detections
bdetects <- findPeaks(bscores)
bdetects
plot(bdetects)
## End(Not run)
# Clean up (only because these files were created in these examples)
file.remove(btnw.fp)
file.remove(oven.fp)
file.remove(survey.fp)
Example output
Loading required package: tuneR
Attaching package: 'monitoR'
The following object is masked from 'package:tuneR':
readMP3
Automatic point selection.
Done.
Automatic point selection.
Done.
Starting w . . .
Fourier transform on survey . . .
Continuing. . .
Done.
Starting o . . .
Done.
Done with w
Done with o
Done
A "detectionList" object
Based on survey file: /work/tmp/tmp/RtmpJaoGTT/survey2010-12-31_120000_EST.wav
and 2 templates
Detection information
n.peaks n.detections min.peak.score max.peak.score min.detection.score
w 38 3 0.009121254 0.7291718 0.4057619
o 5 3 0.168144533 0.6221447 0.4572363
max.detection.score
w 0.7291718
o 0.6221447
0 to 23.5 seconds
plot-methods package:monitoR R Documentation
_M_e_t_h_o_d_s _f_o_r _t_h_e '_p_l_o_t' _F_u_n_c_t_i_o_n
_D_e_s_c_r_i_p_t_i_o_n:
Plotting acoustic templates and template scores
_U_s_a_g_e:
## S4 method for signature 'TemplateList,ANY'
plot(x, which.one = names(x@templates), click = FALSE,
ask = if(length(which.one)>1) TRUE else FALSE, spec.col = gray.3(), on.col = '#FFA50075',
off.col = '#0000FF75', pt.col = '#FFA50075', line.col = 'black')
## S4 method for signature 'detectionList,ANY'
plot(x, flim = c(0, 12), scorelim,
which.one = names(x@templates), box = TRUE, spec.col = gray.2(), t.each = 30,
hit.marker = 'lines',
color = c('red', 'blue', 'green', 'orange', 'purple', 'pink', 'darkgreen', 'turquoise',
'royalblue', 'orchid4', 'brown', 'salmon2'), legend = TRUE, all.peaks = FALSE,
ask = if(dev.list() == 2) TRUE else FALSE)
_A_r_g_u_m_e_n_t_s:
x: A template list ('TemplateList' object) or detection list
('detectionList' object).
which.one: Names of templates to be plotted.
click: Set to 'TRUE' to see values of locations on plot by mouse
clicks.
ask: Set to 'FALSE' to eliminate pause between plots.
spec.col: Color ramp for spectrogram.
on.col: Color for ``on'' points (binary templates only).
off.col: Color for ``off'' points (binary templates only).
pt.col: Color for template points (correlation templates only).
line.col: Color for lines if 'click = TRUE'.
flim: Frequency limits for plot.
scorelim: Score limits for plot.
box: If 'TRUE' boxes are plotted in spectrogram for each
detection.
t.each: Duration shown in each individual plot (s).
hit.marker: Type of marker used to show detections in score plot. Can
be '"lines"' or '"points"'.
color: Colors used for individual templates.
legend: Show legend?
all.peaks: Indicate location of all peaks?
_A_u_t_h_o_r(_s):
Sasha D. Hafner
_S_e_e _A_l_s_o:
'makeCorTemplate', 'makeBinTemplate'
_E_x_a_m_p_l_e_s:
## Not run:
# Not run because of the time required (maybe 5-10 seconds)
# Also some plot calls require user input by default
# Load data
data(btnw)
data(survey)
# Write Wave objects to file (temporary directory used here)
btnw.fp <- file.path(tempdir(), "btnw.wav")
oven.fp <- file.path(tempdir(), "oven.wav")
survey.fp <- file.path(tempdir(), "survey2010-12-31_120000_EST.wav")
writeWave(btnw, btnw.fp)
writeWave(survey, survey.fp)
# Create a template list
ctemp1 <- makeCorTemplate(btnw.fp, name = "w1")
ctemp2 <- makeCorTemplate(btnw.fp, t.lim = c(0.5, 2.5), frq.lim = c(1, 10), dens = 0.1, name = "w2")
ctemps <- combineCorTemplates(ctemp1, ctemp2)
# Then it can be plotted like this
plot(ctemps)
# Next call is not useful for template w1 but good for w2:
plot(ctemps, pt.col = "red")
# Can plot just one template
plot(ctemps, which.one = 2, pt.col = "red")
plot(ctemps, which.one = "w2", pt.col = "red")
# And to check values
plot(ctemps, which.one = 1, click = TRUE)
# To plot detections, let's create some
cscores <- corMatch(survey.fp, ctemps)
cdetects <- findPeaks(cscores)
# And to plot them:
plot(cdetects)
# Clean up (only because these files were created in these examples)
file.remove(btnw.fp)
file.remove(survey.fp)
## End(Not run)
Automatic point selection.
Done.
Automatic point selection.
Done.
Starting w . . .
Fourier transform on survey . . .
Continuing. . .
Done.
Starting o . . .
Done.
Done with w
Done with o
Done
A "detectionList" object
Based on survey file: /work/tmp/tmp/RtmpJaoGTT/survey2010-12-31_120000_EST.wav
and 2 templates
Detection information
n.peaks n.detections min.peak.score max.peak.score min.detection.score
w 31 1 -0.4115253 17.58376 17.58376
o 5 1 3.1192727 18.75724 18.75724
max.detection.score
w 17.58376
o 18.75724
0 to 23.5 seconds
[1] TRUE
[1] TRUE
[1] TRUE
monitoR documentation built on May 1, 2019, 6:28 p.m.
R Package Documentation
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Description Usage Arguments Details Value Author(s) See Also Examples
Description
This function accepts templateScores objects and returns information on all score peaks and those peaks that are considered detections.
Usage
1 2 |
Arguments
score.obj |
A |
fd.rat |
A ratio of frame width (twice minimum peak separation) to template duration. |
frame |
If you want the same frame width for templates with varying duration, specify a value directly.
|
parallel |
Set to |
Details
The findPeaks function translates raw scores from template matching to detection information, by finding peaks in the score data, and determining which peaks, if any, exceed the score cutoffs specified in the templates (see the two functions for making templates, makeBinTemplate and makeCorTemplate and templateCutoff for more details on cutoffs).
Value
An S4 object of class templateScores, with the following slots:
survey.name |
The file path to the survey that the scores apply to. |
survey |
The actual survey as a |
survey.data |
A named list with one element per template. Each element is a named list with time-domain results for the survey. |
templates |
The templates (an S4 object of class |
scores |
A named list with an element for each template. Each element contains the scores for an individual template. |
peaks |
A named list with peak information (as a data frame) for each template. |
detections |
A named list with detection information (as a data frame) for each template. |
Author(s)
Sasha D. Hafner and Jon Katz
See Also
makeCorTemplate,
makeBinTemplate,
corMatch,
binMatch,
getDetections,
getPeaks
Examples
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 | # Load data
data(btnw)
data(oven)
data(survey)
# Write Wave objects to file (temporary directory used here)
btnw.fp <- file.path(tempdir(), "btnw.wav")
oven.fp <- file.path(tempdir(), "oven.wav")
survey.fp <- file.path(tempdir(), "survey2010-12-31_120000_EST.wav")
writeWave(btnw, btnw.fp)
writeWave(oven, oven.fp)
writeWave(survey, survey.fp)
# Correlation example
# Create two correlation templates
wct <- makeCorTemplate(btnw.fp, t.lim = c(1.5, 2.1), frq.lim = c(4.2, 5.6), name = "w")
oct <- makeCorTemplate(oven.fp, t.lim = c(1, 4), frq.lim = c(1, 11), dens = 0.1, name = "o")
# Combine them
ctemps <- combineCorTemplates(wct, oct)
# Calculate scores
cscores <- corMatch(survey.fp, ctemps)
# Finally, find peaks and detections
cdetects <- findPeaks(cscores)
cdetects
plot(cdetects)
# plotting help:
method?plot('detectionList')
# Binary example
## Not run:
# Not run because of the time required (maybe 2-5 seconds) Create two templates
wbt <- makeBinTemplate(btnw.fp, amp.cutoff = -30, t.lim = c(1.5, 2.1), frq.lim = c(4.2, 5.6),
buffer = 2, name = "w")
obt <- makeBinTemplate(oven.fp, amp.cutoff = -20, t.lim = c(1, 4), frq.lim = c(1, 11),
name = "o")
# Combine them
btemps <- combineBinTemplates(wbt, obt)
# Calculate scores
bscores <- binMatch(survey.fp, btemps)
# Finally, find peaks and detections
bdetects <- findPeaks(bscores)
bdetects
plot(bdetects)
## End(Not run)
# Clean up (only because these files were created in these examples)
file.remove(btnw.fp)
file.remove(oven.fp)
file.remove(survey.fp)
|
Example output
Loading required package: tuneR
Attaching package: 'monitoR'
The following object is masked from 'package:tuneR':
readMP3
Automatic point selection.
Done.
Automatic point selection.
Done.
Starting w . . .
Fourier transform on survey . . .
Continuing. . .
Done.
Starting o . . .
Done.
Done with w
Done with o
Done
A "detectionList" object
Based on survey file: /work/tmp/tmp/RtmpJaoGTT/survey2010-12-31_120000_EST.wav
and 2 templates
Detection information
n.peaks n.detections min.peak.score max.peak.score min.detection.score
w 38 3 0.009121254 0.7291718 0.4057619
o 5 3 0.168144533 0.6221447 0.4572363
max.detection.score
w 0.7291718
o 0.6221447
0 to 23.5 seconds
plot-methods package:monitoR R Documentation
_M_e_t_h_o_d_s _f_o_r _t_h_e '_p_l_o_t' _F_u_n_c_t_i_o_n
_D_e_s_c_r_i_p_t_i_o_n:
Plotting acoustic templates and template scores
_U_s_a_g_e:
## S4 method for signature 'TemplateList,ANY'
plot(x, which.one = names(x@templates), click = FALSE,
ask = if(length(which.one)>1) TRUE else FALSE, spec.col = gray.3(), on.col = '#FFA50075',
off.col = '#0000FF75', pt.col = '#FFA50075', line.col = 'black')
## S4 method for signature 'detectionList,ANY'
plot(x, flim = c(0, 12), scorelim,
which.one = names(x@templates), box = TRUE, spec.col = gray.2(), t.each = 30,
hit.marker = 'lines',
color = c('red', 'blue', 'green', 'orange', 'purple', 'pink', 'darkgreen', 'turquoise',
'royalblue', 'orchid4', 'brown', 'salmon2'), legend = TRUE, all.peaks = FALSE,
ask = if(dev.list() == 2) TRUE else FALSE)
_A_r_g_u_m_e_n_t_s:
x: A template list ('TemplateList' object) or detection list
('detectionList' object).
which.one: Names of templates to be plotted.
click: Set to 'TRUE' to see values of locations on plot by mouse
clicks.
ask: Set to 'FALSE' to eliminate pause between plots.
spec.col: Color ramp for spectrogram.
on.col: Color for ``on'' points (binary templates only).
off.col: Color for ``off'' points (binary templates only).
pt.col: Color for template points (correlation templates only).
line.col: Color for lines if 'click = TRUE'.
flim: Frequency limits for plot.
scorelim: Score limits for plot.
box: If 'TRUE' boxes are plotted in spectrogram for each
detection.
t.each: Duration shown in each individual plot (s).
hit.marker: Type of marker used to show detections in score plot. Can
be '"lines"' or '"points"'.
color: Colors used for individual templates.
legend: Show legend?
all.peaks: Indicate location of all peaks?
_A_u_t_h_o_r(_s):
Sasha D. Hafner
_S_e_e _A_l_s_o:
'makeCorTemplate', 'makeBinTemplate'
_E_x_a_m_p_l_e_s:
## Not run:
# Not run because of the time required (maybe 5-10 seconds)
# Also some plot calls require user input by default
# Load data
data(btnw)
data(survey)
# Write Wave objects to file (temporary directory used here)
btnw.fp <- file.path(tempdir(), "btnw.wav")
oven.fp <- file.path(tempdir(), "oven.wav")
survey.fp <- file.path(tempdir(), "survey2010-12-31_120000_EST.wav")
writeWave(btnw, btnw.fp)
writeWave(survey, survey.fp)
# Create a template list
ctemp1 <- makeCorTemplate(btnw.fp, name = "w1")
ctemp2 <- makeCorTemplate(btnw.fp, t.lim = c(0.5, 2.5), frq.lim = c(1, 10), dens = 0.1, name = "w2")
ctemps <- combineCorTemplates(ctemp1, ctemp2)
# Then it can be plotted like this
plot(ctemps)
# Next call is not useful for template w1 but good for w2:
plot(ctemps, pt.col = "red")
# Can plot just one template
plot(ctemps, which.one = 2, pt.col = "red")
plot(ctemps, which.one = "w2", pt.col = "red")
# And to check values
plot(ctemps, which.one = 1, click = TRUE)
# To plot detections, let's create some
cscores <- corMatch(survey.fp, ctemps)
cdetects <- findPeaks(cscores)
# And to plot them:
plot(cdetects)
# Clean up (only because these files were created in these examples)
file.remove(btnw.fp)
file.remove(survey.fp)
## End(Not run)
Automatic point selection.
Done.
Automatic point selection.
Done.
Starting w . . .
Fourier transform on survey . . .
Continuing. . .
Done.
Starting o . . .
Done.
Done with w
Done with o
Done
A "detectionList" object
Based on survey file: /work/tmp/tmp/RtmpJaoGTT/survey2010-12-31_120000_EST.wav
and 2 templates
Detection information
n.peaks n.detections min.peak.score max.peak.score min.detection.score
w 31 1 -0.4115253 17.58376 17.58376
o 5 1 3.1192727 18.75724 18.75724
max.detection.score
w 17.58376
o 18.75724
0 to 23.5 seconds
[1] TRUE
[1] TRUE
[1] TRUE
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We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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