The Rraven package is designed to facilitate the exchange of data between R and Raven sound analysis software (Cornell Lab of Ornithology). Raven provides very powerful tools for the analysis of (animal) sounds. R can simplify the automatization of complex routines of analyses. Furthermore, R packages as warbleR, seewave and monitoR (among others) provide additional methods of analysis, working as a perfect complement for those found in Raven. Hence, bridging these applications can largely expand the bioacoustician’s toolkit.

Currently, most analyses in Raven cannot be run in the background from a command terminal. Thus, most Rraven functions are design to simplify the exchange of data between the two programs, and in some cases, export files to Raven for further analysis. This vignette provides detailed examples for each function in Rraven, including both the R code as well as the additional steps in Raven required to fully accomplished the analyses. Raven Pro must be installed to be able to run some of the code. Note that the animations explaining these additional Raven steps are shown in more detail in the github version of this vignette, which can be downloaded as follows (saves the file “Rraven.github.html” in your current working directory):

download.file(
  url = "https://raw.githubusercontent.com/maRce10/Rraven/master/gifs/Rraven.hitgub.html", 
  destfile = "Rraven.github.html")

 

The downloaded file can be opened by any internet browser.

Before getting into the functions, the packages must be installed and loaded. I recommend using the latest developmental version, which is found in github. To do so, you need the R package devtools (which of course should be installed!). Some warbleR functions and example data sets will be used, so warbleR should be installed as well:

devtools::install_github("maRce10/warbleR")

devtools::install_github("maRce10/Rraven")

#from CRAN would be
#install.packages("warbleR")

#load packages
library(warbleR)
library(Rraven)

 

Let’s also use a temporary folder as the working directory in which to save all sound files and data files:

setwd(tempdir())

#load example data
data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4", "selec.table", "selection_files"))

#save sound files  in temporary directory
writeWave(Phae.long1, "Phae.long1.wav", extensible = FALSE)
writeWave(Phae.long2, "Phae.long2.wav", extensible = FALSE)
writeWave(Phae.long3, "Phae.long3.wav", extensible = FALSE)
writeWave(Phae.long4, "Phae.long4.wav", extensible = FALSE)

#save Raven selection tables in the temporary directory
out <- lapply(1:4, function(x)
writeLines(selection_files[[x]], con = names(selection_files)[x]))

#this is the temporary directory location (of course different each time is run)
getwd() 

 


Importing data from Raven

imp_raven

This function imports Raven selection tables. Multiple files can be imported at once. Raven selection tables including data from multiple recordings can also be imported. It returns a single data frame with the information contained in the selection files. We already have 2 Raven selection tables in the working directory:

list.files(path = tempdir(), pattern = "\\.txt$")
[1] "LBH 1 selection table example.txt" "LBH 2 selection table example.txt" "LBH 3 selection table example.txt" "LBH 4 selection table example.txt"

 

This code shows how to import all the data contained in those files into R:

 #providing the name of the column with the sound file names
rvn.dat <- imp_raven(all.data = TRUE, path = tempdir())

head(rvn.dat)
Selection View Channel Begin Time (s) End Time (s) Low Freq (Hz) High Freq (Hz) Begin File channel Begin Path File Offset (s) File Offset selec.file
1 Spectrogram 1 1 1.1693549 1.3423884 2220.105 8604.378 Phae.long1.wav 1 /tmp/RtmpWpOeaR/Phae.long1.wav 1.1693549 NA LBH 1 selection table example.txt
2 Spectrogram 1 1 2.1584085 2.3214565 2169.437 8807.053 Phae.long1.wav 1 /tmp/RtmpWpOeaR/Phae.long1.wav 2.1584085 NA LBH 1 selection table example.txt
3 Spectrogram 1 1 0.3433366 0.5182553 2218.294 8756.604 Phae.long1.wav 1 /tmp/RtmpWpOeaR/Phae.long1.wav 0.3433366 NA LBH 1 selection table example.txt
1 Spectrogram 1 1 0.1595983 0.2921692 2316.862 8822.316 Phae.long2.wav 1 /tmp/RtmpWpOeaR/Phae.long2.wav 0.1595983 NA LBH 2 selection table example.txt
2 Spectrogram 1 1 1.4570585 1.5832087 2284.006 8888.027 Phae.long2.wav 1 /tmp/RtmpWpOeaR/Phae.long2.wav 1.4570585 NA LBH 2 selection table example.txt
1 Spectrogram 1 1 0.6265520 0.7577715 3006.834 8822.316 Phae.long3.wav 1 /tmp/RtmpWpOeaR/Phae.long3.wav NA 0.626552 LBH 3 selection table example.txt

 

Note that the ‘waveform’ view data has been removed. It can also be imported as follows (but note that the example selection tables have no waveform data):

rvn.dat <- imp_raven(all.data = TRUE, waveform = TRUE, 
                     path = tempdir())

 

Raven selections can also be imported in a ‘selection.table’ format so it can be directly input into warbleR functions. To do this you need to set warbler.format = TRUE:

 #providing the name of the column with the sound file names
rvn.dat <- imp_raven(sound.file.col = "End.File", 
                     warbler.format =  TRUE, path = tempdir())

head(rvn.dat)
selec Channel start end bottom.freq top.freq sound.files channel selec.file
1 1 1.169355 1.342388 2.22011 8.60438 Phae.long1.wav 1 LBH 1 selection table example.txt
2 1 2.158408 2.321457 2.16944 8.80705 Phae.long1.wav 1 LBH 1 selection table example.txt
3 1 0.343337 0.518255 2.21829 8.75660 Phae.long1.wav 1 LBH 1 selection table example.txt
1 1 0.159598 0.292169 2.31686 8.82232 Phae.long2.wav 1 LBH 2 selection table example.txt
2 1 1.457058 1.583209 2.28401 8.88803 Phae.long2.wav 1 LBH 2 selection table example.txt
1 1 0.626552 0.757771 3.00683 8.82232 Phae.long3.wav 1 LBH 3 selection table example.txt

 

The data frame contains the following columns: sound.files, channel, selec, start, end, and selec.file. You can also import the frequency range parameters in the ‘selection.table’ by setting ‘freq.cols’ tp TRUE. The data frame returned by “imp_raven” (when in the ‘warbleR’ format) can be input into several warbleR functions for further analysis. For instance, the following code runs additional parameter measurements on the imported selections:

# convert to class selection.table
rvn.dat.st <- selection_table(rvn.dat, path = tempdir())

sp <- spectro_analysis(X = rvn.dat, bp = "frange", wl = 150, 
             pb = FALSE, ovlp = 90, path = tempdir())

head(sp)
checking selections (step 1 of 2):
all selections are OK 
sound.files selec duration meanfreq sd freq.median freq.Q25 freq.Q75 freq.IQR time.median time.Q25 time.Q75 time.IQR skew kurt sp.ent time.ent entropy sfm meandom mindom maxdom dfrange modindx startdom enddom dfslope meanpeakf
Phae.long1.wav 1 0.173033 5.98235 1.39969 6.33172 5.29658 6.86952 1.57294 0.076455 0.046568 0.117463 0.070895 1.99804 7.02156 0.943429 0.886904 0.836731 0.651002 6.49105 3.825 8.325 4.50 7.20000 6.975 7.575 3.46754 7.125
Phae.long1.wav 2 0.163048 5.99730 1.42293 6.21213 5.32875 6.88079 1.55205 0.076655 0.043903 0.115680 0.071777 1.91836 7.33432 0.946822 0.888565 0.841313 0.667865 6.71394 3.975 8.475 4.50 4.90000 6.825 7.275 2.75992 6.975
Phae.long1.wav 3 0.174919 6.02060 1.51554 6.42844 5.15281 6.98331 1.83050 0.090243 0.053452 0.127729 0.074277 2.49536 11.13912 0.945082 0.886654 0.837961 0.671589 6.53271 2.325 8.625 6.30 10.30952 2.925 7.275 24.86869 7.125
Phae.long2.wav 1 0.132571 6.39830 1.34041 6.59597 5.60732 7.38085 1.77353 0.076867 0.054300 0.103665 0.049364 1.56852 6.01639 0.942466 0.895480 0.843959 0.608618 6.48287 4.875 8.025 3.15 11.47619 4.875 6.225 10.18323 7.425
Phae.long2.wav 2 0.126150 6.31184 1.37004 6.60202 5.60983 7.21321 1.60338 0.076103 0.052849 0.097947 0.045098 2.46900 10.88435 0.935771 0.897677 0.840020 0.615104 6.17614 3.075 7.725 4.65 9.58065 5.625 5.775 1.18906 6.675
Phae.long3.wav 1 0.131220 6.61240 1.09312 6.67013 6.06721 7.34937 1.28215 0.063505 0.043043 0.089613 0.046571 1.77369 6.62602 0.930244 0.895888 0.833394 0.570215 6.75629 4.875 8.175 3.30 11.04546 5.475 8.025 19.43308 6.675

 

And this code creates song catalogs:

# create a color palette
trc <- function(n) terrain.colors(n = n, alpha = 0.3)

# plot catalog
catalog(X = rvn.dat.st[1:9, ], flim = c(1, 10), nrow = 3, ncol = 3, 
        same.time.scale = TRUE,  spec.mar = 1, box = FALSE,
        ovlp = 90, parallel = 1, mar = 0.01, wl = 200, 
        pal = reverse.heat.colors, width = 20,
        labels = c("sound.files", "selec"), legend = 1, 
        tag.pal = list(trc),  group.tag = "sound.files", path = tempdir())


This is just to mention a few analysis that can be implemented in warbleR.

Rraven also contains the function imp_syrinx to import selections from Syrinx sound analysis software (although this program is not been maintained any longer).

extract_ts

The function extracts parameters encoded as time series in Raven selection tables. The resulting data frame can be directly input into functions for time series analysis of acoustic signals as in the warbleR function freq_DTW. The function needs an R data frame, so the data should have been previously imported using imp_raven. This example uses the selection_file.ts example data that comes with Rraven:

#remove previous raven data files
unlink(list.files(pattern = "\\.txt$", path = tempdir()))

#save Raven selection table in the temporary directory
writeLines(selection_files[[5]], con = file.path(tempdir(), 
                                        names(selection_files)[5]))

rvn.dat <- imp_raven(all.data = TRUE, path = tempdir()) 

# Peak freq contour dif length
fcts <- extract_ts(X = rvn.dat, ts.column = "Peak Freq Contour (Hz)")
 
head(fcts)
sound.files selec PFC..1 PFC..2 PFC..3 PFC..4 PFC..5 PFC..6 PFC..7 PFC..8 PFC..9 PFC..10 PFC..11 PFC..12 PFC..13 PFC..14 PFC..15 PFC..16 PFC..17 PFC..18 PFC..19 PFC..20 PFC..21 PFC..22 PFC..23 PFC..24 PFC..25 PFC..26 PFC..27 PFC..28 PFC..29 PFC..30 PFC..31 PFC..32 PFC..33 PFC..34 PFC..35 PFC..36 PFC..37 PFC..38 PFC..39 PFC..40 PFC..41 PFC..42 PFC..43 PFC..44 PFC..45 PFC..46 PFC..47 PFC..48 PFC..49 PFC..50 PFC..51
Phae.long1.wav 1 6943.4 7119.1 7294.9 7294.9 7294.9 7382.8 7470.7 7646.5 5185.5 5273.4 5361.3 5449.2 5449.2 5537.1 5537.1 5712.9 6416.0 6591.8 6591.8 5976.6 6503.9 5712.9 6416.0 6240.2 5976.6 6328.1 5185.5 5009.8 4658.2 4306.6 3955.1 7119.1 6855.5 6767.6 6767.6 6855.5 6943.4 7119.1 7207.0 7207.0 7207.0 7031.2 6943.4 6591.8 7119.1 7119.1 7207.0 7119.1 7207.0 7119.1 7119.1
Phae.long1.wav 2 6767.6 6943.4 7207.0 7207.0 7294.9 7382.8 7470.7 7558.6 7558.6 7646.5 5185.5 5361.3 5537.1 8261.7 8261.7 8349.6 5800.8 6152.3 6591.8 6679.7 5888.7 6416.0 5625.0 6152.3 5976.6 5976.6 5976.6 5273.4 5273.4 4570.3 4306.6 3867.2 7119.1 6855.5 6855.5 6855.5 6943.4 7119.1 7207.0 7207.0 7207.0 7207.0 7207.0 7119.1 7119.1 7207.0 7119.1 7207.0 NA NA NA
Phae.long1.wav 3 6943.4 4746.1 7119.1 4834.0 7207.0 4921.9 4921.9 7558.6 7646.5 7734.4 7998.0 8085.9 5449.2 8085.9 8349.6 7998.0 8701.2 6503.9 6591.8 5800.8 6503.9 6503.9 6328.1 6416.0 5449.2 6152.3 5361.3 5273.4 4921.9 4482.4 4130.9 3779.3 6943.4 6767.6 6767.6 6767.6 6943.4 7031.2 7119.1 7031.2 7294.9 7207.0 7207.0 7031.2 7207.0 7031.2 7031.2 7119.1 7119.1 7207.0 7119.1
Phae.long2.wav 4 5888.7 6503.9 4570.3 4834.0 5185.5 5537.1 5537.1 5800.8 6503.9 3779.3 6240.2 6328.1 6416.0 6591.8 5273.4 5712.9 4921.9 7382.8 6064.5 6767.6 7646.5 5800.8 7470.7 7294.9 7382.8 5537.1 6152.3 6416.0 5888.7 7558.6 7207.0 7294.9 6591.8 7822.3 7822.3 5976.6 6064.5 6152.3 6152.3 NA NA NA NA NA NA NA NA NA NA NA NA
Phae.long2.wav 5 4570.3 4746.1 4921.9 5097.7 5097.7 5185.5 5800.8 5712.9 5888.7 5976.6 6064.5 6064.5 4570.3 6855.5 6855.5 5976.6 6855.5 6679.7 6328.1 7646.5 5712.9 7207.0 6679.7 6591.8 6240.2 6855.5 6943.4 6416.0 6943.4 6591.8 6503.9 6416.0 7558.6 6591.8 5712.9 6591.8 5537.1 NA NA NA NA NA NA NA NA NA NA NA NA NA NA
Phae.long3.wav 6 4218.8 6240.2 6591.8 6679.7 7119.1 5009.8 5800.8 6240.2 6767.6 6416.0 6328.1 6328.1 6503.9 6679.7 6591.8 5537.1 6679.7 6679.7 6591.8 6943.4 5976.6 6591.8 7119.1 6767.6 7470.7 6416.0 7470.7 6591.8 7998.0 7119.1 7910.2 7031.2 6943.4 7470.7 6943.4 7734.4 7119.1 7822.3 6416.0 6855.5 NA NA NA NA NA NA NA NA NA NA NA

 

Note that these sequences are not all of equal length (one has NAs at the end). extract_ts can also interpolate values so all time series have the same length:

# Peak freq contour equal length
fcts <- extract_ts(X = rvn.dat, ts.column = "Peak Freq Contour (Hz)",  equal.length = TRUE)

#look at the last rows wit no NAs
head(fcts)
sound.files selec PFC..1 PFC..2 PFC..3 PFC..4 PFC..5 PFC..6 PFC..7 PFC..8 PFC..9 PFC..10 PFC..11 PFC..12 PFC..13 PFC..14 PFC..15 PFC..16 PFC..17 PFC..18 PFC..19 PFC..20 PFC..21 PFC..22 PFC..23 PFC..24 PFC..25 PFC..26 PFC..27 PFC..28 PFC..29 PFC..30
Phae.long1.wav 1 6943.4 7246.40 7294.90 7397.96 7628.31 5240.06 5391.61 5455.26 5537.10 6076.57 6591.80 5997.81 5958.38 6343.26 6025.08 5343.10 4803.69 4197.51 7110.01 6788.82 6810.03 6979.75 7200.94 7207.00 6997.90 6646.35 7119.10 7158.50 7182.75 7119.1
Phae.long1.wav 2 6767.6 7107.01 7228.22 7370.68 7513.13 7567.69 5864.40 5421.92 8167.75 8313.23 5873.52 6516.02 6325.11 6361.45 5988.66 5976.60 5976.60 5273.40 4524.83 3958.11 7010.02 6855.50 6913.09 7143.35 7207.00 7207.00 7194.88 7119.10 7173.66 7207.0
Phae.long1.wav 3 6943.4 6464.48 5897.76 4921.90 7285.84 7701.06 8028.31 5631.04 8295.04 8361.72 6525.12 5828.08 6503.90 6364.47 5546.18 5470.40 5067.35 4373.31 3888.41 6810.03 6767.60 6961.57 7113.04 7203.97 7207.00 7049.39 7061.51 7079.70 7143.35 7119.1
Phae.long2.wav 4 5888.7 5903.82 4733.98 5161.26 5537.10 5682.59 6406.92 4203.59 6282.63 6397.81 6455.41 5455.26 5140.11 7337.34 6306.95 7343.43 5864.44 7422.20 7346.43 5728.03 6206.86 6143.26 7270.69 7219.12 6979.72 7525.28 7695.01 6009.94 6125.05 6152.3
Phae.long2.wav 5 4570.3 4788.53 5006.77 5097.70 5182.47 5782.61 5791.71 5949.32 6058.44 5806.88 5515.90 6855.50 6067.52 6831.25 6546.33 7146.42 5979.60 7152.45 6649.39 6385.69 6749.41 6907.03 6579.68 6749.41 6522.09 6455.40 7291.90 6137.20 6379.65 5537.1
Phae.long3.wav 6 4218.8 6361.44 6652.42 7046.37 5309.83 6118.99 6743.35 6379.63 6328.10 6522.09 6640.30 5755.31 6679.70 6637.27 6882.78 6082.67 6864.54 6816.08 7252.49 6997.90 6682.72 7785.85 7582.85 7091.82 7088.86 7143.41 7707.12 7337.33 6900.93 6855.5

 

And the length of the series can also be specified:

# Peak freq contour equal length 10 measurements
fcts <- extract_ts(X = rvn.dat, ts.column = "Peak Freq Contour (Hz)",
equal.length = T, length.out = 10)  

head(fcts)
sound.files selec PFC..1 PFC..2 PFC..3 PFC..4 PFC..5 PFC..6 PFC..7 PFC..8 PFC..9 PFC..10
Phae.long1.wav 1 6943.4 7431.63 5449.20 6533.20 6376.93 4736.33 6767.60 7207.00 7119.10 7119.1
Phae.long1.wav 2 6767.6 7402.33 5263.63 6650.40 6357.41 5898.47 4951.17 7041.01 7207.00 7207.0
Phae.long1.wav 3 6943.4 4921.90 7792.93 7236.33 6347.63 5000.01 6767.60 7040.97 7128.87 7119.1
Phae.long2.wav 4 5888.7 5263.63 5292.97 6533.20 7109.37 5986.34 5742.17 7363.27 7822.30 6152.3
Phae.long2.wav 5 4570.3 5097.70 5888.70 4570.30 6855.50 5712.90 6240.20 6943.40 7558.60 5537.1
Phae.long3.wav 6 4218.8 6416.00 6533.20 6679.70 6650.40 6943.33 7470.70 7617.20 7470.73 6855.5

 

The time series data frame can be directly input into the freq_DTW warbleR function to calculate Dynamic Time Warping distances:

freq_DTW(ts.df = fcts, path = tempdir())

 

Phae.long1.wav-1 Phae.long1.wav-2 Phae.long1.wav-3 Phae.long2.wav-4 Phae.long2.wav-5 Phae.long3.wav-6 Phae.long3.wav-7 Phae.long3.wav-8 Phae.long4.wav-9 Phae.long4.wav-10 Phae.long4.wav-11
Phae.long1.wav-1 0.00 2509.73 5702.99 9541.19 12411.93 9648.40 7207.00 7343.82 13740.28 11455.40 14970.64
Phae.long1.wav-2 2509.73 0.00 5624.78 7334.11 12333.71 10058.78 7255.63 7734.49 14257.91 10908.22 15107.31
Phae.long1.wav-3 5702.99 5624.78 0.00 10615.03 11620.86 11044.99 8046.64 7675.46 15077.77 13476.38 14696.92
Phae.long2.wav-4 9541.19 7334.11 10615.03 0.00 7665.76 9111.46 7587.78 7109.27 11318.26 10683.49 11572.13
Phae.long2.wav-5 12411.93 12333.71 11620.86 7665.76 0.00 8466.93 9160.36 8339.72 10839.78 13535.00 9902.21
Phae.long3.wav-6 9648.40 10058.78 11044.99 9111.46 8466.93 0.00 6464.63 6425.53 16122.97 15234.57 14413.98
Phae.long3.wav-7 7207.00 7255.63 8046.64 7587.78 9160.36 6464.63 0.00 4882.82 13144.40 11689.30 13095.31
Phae.long3.wav-8 7343.82 7734.49 7675.46 7109.27 8339.72 6425.53 4882.82 0.00 13711.03 13144.48 13515.51
Phae.long4.wav-9 13740.28 14257.91 15077.77 11318.26 10839.78 16122.97 13144.40 13711.03 0.00 10517.49 9424.16
Phae.long4.wav-10 11455.40 10908.22 13476.38 10683.49 13535.00 15234.57 11689.30 13144.48 10517.49 0.00 9725.81
Phae.long4.wav-11 14970.64 15107.31 14696.92 11572.13 9902.21 14413.98 13095.31 13515.51 9424.16 9725.81 0.00

relabel_colms

This is a simple function to relabel columns so they match the selection table format used in warbleR:

#to simplify the example select a subset of the columns 
st1 <- rvn.dat[ ,1:7]

#check original column names
st1
# Relabel the basic columns required by warbleR
relabel_colms(st1)

 

Additional columns can also be relabeled:

# 2 additional column 
relabel_colms(st1, extra.cols.name = "View",
              extra.cols.new.name = "Raven view")
selec Raven view Channel start end bottom.freq top.freq
1 Spectrogram 1 1 1.169 1.342033 2220.1 8604.4
2 Spectrogram 1 1 2.158 2.321048 2169.4 8807.1
3 Spectrogram 1 1 0.343 0.517919 2218.3 8756.6
4 Spectrogram 1 1 0.160 0.292571 2316.9 8822.3
5 Spectrogram 1 1 1.457 1.583150 2284.0 8888.0
6 Spectrogram 1 1 0.627 0.758220 3006.8 8822.3
7 Spectrogram 1 1 1.974 2.104179 2776.8 8888.0
8 Spectrogram 1 1 0.123 0.254217 2316.9 9315.2
9 Spectrogram 1 1 1.517 1.662425 2514.0 9216.6
10 Spectrogram 1 1 2.933 3.077186 2579.7 10235.1
11 Spectrogram 1 1 0.145 0.290099 2579.7 9742.3

 


imp_corr_mat

The function imports the output of a batch correlation routine in Raven. Both the correlation and lag matrices contained in the output ‘.txt’ file are read and both waveform and spectrogram (cross-correlation) correlations can be imported.

This example shows how to input the sound files into Raven and how to bring the results back to R. First, the selections need to be cut as single sound files for the Raven correlator to be able to read it. We can do this using the cut_sels function from warbleR:

#create new folder to put cuts
dir.create(file.path(tempdir(), "cuts"))

# add a rowname column to be able to match cuts and selections
selec.table$rownames <- sprintf("%02d",1:nrow(selec.table))

# cut files
cut_sels(X = selec.table, mar = 0.05, path = tempdir(), dest.path = 
           file.path(tempdir(), "cuts"), 
         labels = c("rownames", "sound.files", "selec"), pb = FALSE)

#list cuts
list.files(path = file.path(tempdir(), "cuts"))

 

Every selection is in its own sound file (labeled as paste("rownames", "sound.files", "selec")). Now open Raven and run the batch correlator on the ‘cuts’ folder as follows:

gif1  

And then import the output file into R:

# Import output (change the name of the file if you used a different one)
xcorr.rav <- imp_corr_mat(file = "BatchCorrOutput.txt", path = tempdir())

 

The function returns a list containing the correlation matrix:

xcorr.rav$correlation

 

01-Phae.long1-1.wav 10-Phae.long4-2.wav 11-Phae.long4-3.wav 07-Phae.long3-2.wav 05-Phae.long2-2.wav 09-Phae.long4-1.wav 04-Phae.long2-1.wav 02-Phae.long1-2.wav 06-Phae.long3-1.wav 03-Phae.long1-3.wav 08-Phae.long3-3.wav
01-Phae.long1-1.wav 1.000 0.216 0.184 0.285 0.443 0.195 0.145 0.613 0.360 0.812 0.236
10-Phae.long4-2.wav 0.216 1.000 0.781 0.290 0.235 0.907 0.289 0.176 0.204 0.209 0.323
11-Phae.long4-3.wav 0.184 0.781 1.000 0.279 0.186 0.804 0.274 0.127 0.189 0.185 0.393
07-Phae.long3-2.wav 0.285 0.290 0.279 1.000 0.433 0.281 0.270 0.251 0.635 0.274 0.496
05-Phae.long2-2.wav 0.443 0.235 0.186 0.433 1.000 0.197 0.243 0.449 0.397 0.363 0.304
09-Phae.long4-1.wav 0.195 0.907 0.804 0.281 0.197 1.000 0.310 0.164 0.199 0.214 0.322
04-Phae.long2-1.wav 0.145 0.289 0.274 0.270 0.243 0.310 1.000 0.151 0.302 0.182 0.256
02-Phae.long1-2.wav 0.613 0.176 0.127 0.251 0.449 0.164 0.151 1.000 0.264 0.448 0.200
06-Phae.long3-1.wav 0.360 0.204 0.189 0.635 0.397 0.199 0.302 0.264 1.000 0.318 0.377
03-Phae.long1-3.wav 0.812 0.209 0.185 0.274 0.363 0.214 0.182 0.448 0.318 1.000 0.227
08-Phae.long3-3.wav 0.236 0.323 0.393 0.496 0.304 0.322 0.256 0.200 0.377 0.227 1.000

 

and the time lag matrix:

xcorr.rav$`lag (s)`

 

01-Phae.long1-1.wav 10-Phae.long4-2.wav 11-Phae.long4-3.wav 07-Phae.long3-2.wav 05-Phae.long2-2.wav 09-Phae.long4-1.wav 04-Phae.long2-1.wav 02-Phae.long1-2.wav 06-Phae.long3-1.wav 03-Phae.long1-3.wav 08-Phae.long3-3.wav
01-Phae.long1-1.wav 0.000 0.011 0.006 0.028 0.034 0.006 0.023 0.000 0.023 -0.006 0.023
10-Phae.long4-2.wav -0.011 0.000 -0.006 0.040 0.023 -0.006 -0.028 -0.017 0.040 -0.017 0.057
11-Phae.long4-3.wav -0.006 0.006 0.000 0.046 0.028 0.000 -0.023 -0.074 0.046 -0.011 0.063
07-Phae.long3-2.wav -0.028 -0.040 -0.046 0.000 -0.011 -0.046 -0.023 -0.034 0.000 -0.028 0.017
05-Phae.long2-2.wav -0.034 -0.023 -0.028 0.011 0.000 -0.028 0.017 -0.028 0.023 -0.040 0.006
09-Phae.long4-1.wav -0.006 0.006 0.000 0.046 0.028 0.000 -0.023 0.034 0.046 -0.011 0.063
04-Phae.long2-1.wav -0.023 0.028 0.023 0.023 -0.017 0.023 0.000 -0.057 0.057 -0.051 0.017
02-Phae.long1-2.wav 0.000 0.017 0.074 0.034 0.028 -0.034 0.057 0.000 0.040 0.000 0.023
06-Phae.long3-1.wav -0.023 -0.040 -0.046 0.000 -0.023 -0.046 -0.057 -0.040 0.000 -0.028 0.000
03-Phae.long1-3.wav 0.006 0.017 0.011 0.028 0.040 0.011 0.051 0.000 0.028 0.000 0.023
08-Phae.long3-3.wav -0.023 -0.057 -0.063 -0.017 -0.006 -0.063 -0.017 -0.023 0.000 -0.023 0.000

 

This output is ready for stats. For instance, the following code runs a mantel test between cross-correlation (converted to distances) and warbleR spectral parameter pairwise dissimilarities:

#convert cross-corr to distance
xcorr.rvn <- 1- xcorr.rav$correlation

#sort matrix to match selection table
xcorr.rvn <- xcorr.rvn[order(rownames(xcorr.rvn)), order(colnames(xcorr.rvn))]

#convert it to distance matrix
xcorr.rvn <- as.dist(xcorr.rvn)

# measure acoustic parameters
sp.wrblR <- specan(selec.table, bp = c(1, 11), wl = 150, 
                   pb = FALSE, path = tempdir())

#convert them to distance matrix
dist.sp.wrblR <- dist(sp.wrblR)
Warning in dist(sp.wrblR): NAs introduced by coercion
vegan::mantel(xcorr.rvn, dist.sp.wrblR)

Mantel statistic based on Pearson's product-moment correlation 

Call:
vegan::mantel(xdis = xcorr.rvn, ydis = dist.sp.wrblR) 

Mantel statistic r: 0.259 
      Significance: 0.013 

Upper quantiles of permutations (null model):
  90%   95% 97.5%   99% 
0.142 0.180 0.216 0.270 
Permutation: free
Number of permutations: 999

 

There is actually a good match between the two methods!


Exporting R data to Raven

exp_raven

exp_raven saves a selection table in ‘.txt’ format that can be directly opened in Raven. No objects are returned into the R environment. The following code exports a data table from a single sound file:

# Select data for a single sound file
st1 <- selec.table[selec.table$sound.files == "Phae.long1.wav", ]

# Export data of a single sound file
exp_raven(st1, file.name = "Phaethornis 1", khz.to.hz = TRUE, path = tempdir())

 

If the path to the sound file is provided, the functions exports a ‘sound selection table’ which can be directly open by Raven (and which will also open the associated sound file):

# Select data for a single sound file
st1 <- selec.table[selec.table$sound.files == "Phae.long1.wav",]

# Export data of a single sound file
exp_raven(st1, file.name = "Phaethornis 1", khz.to.hz = TRUE,
          sound.file.path = tempdir(), path = tempdir())

gif2  

This is useful to add new selections or even new measurements:

gif3  

If several sound files are available, users can either export them as a single selection file or as multiple selection files (one for each sound file). This example creates a multiple sound file selection:

exp_raven(X = selec.table, file.name = "Phaethornis multiple sound files", 
          sound.file.path = tempdir(), single.file = TRUE, path = tempdir())

 

These type of tables can be opened as a multiple file display in Raven.


Running Raven from R

run_raven

The function opens multiple sound files simultaneously in Raven. When the analysis is finished (and the Raven window is closed) the data can be automatically imported back into R using the ‘import’ argument. Note that Raven, unlike R, can also handle files in ‘mp3’, ‘flac’ and ‘aif’ format .

# here replace with the path where Raven is install in your computer
raven.path <- "PATH_TO_RAVEN_DIRECTORY_HERE" 

# run function 
run_raven(raven.path = raven.path, sound.files = c("Phae.long1.wav", "Phae.long2.wav", "Phae.long3.wav", "Phae.long4.wav"), 
          import = TRUE, all.data = TRUE, path = tempdir())  

gif5  

See imp_raven above for more details on additional settings when importing selections.


raven_batch_detec

As the name suggests, raven_batch_detec runs Raven detector on multiple sound files (sequentially). Batch detection in Raven can also take files in ‘mp3’, ‘flac’ and ‘aif’ format (although this could not be further analyzed in R!).

This is example runs the detector on one of the example sound files that comes by default with Raven:

detec.res <- raven_batch_detec(raven.path = raven.path, 
                               sound.files = "BlackCappedVireo.aif",
                               path = file.path(raven.path, "Examples"))

gif6  


Please report any bugs here. The Rraven package should be cited as follows:

Araya-Salas, M. (2017), Rraven: connecting R and Raven bioacoustic software. R package version 1.0.0.


Session information

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.1 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3

locale:
 [1] LC_CTYPE=pt_PT.UTF-8       LC_NUMERIC=C               LC_TIME=es_CR.UTF-8        LC_COLLATE=C               LC_MONETARY=es_CR.UTF-8   
 [6] LC_MESSAGES=pt_PT.UTF-8    LC_PAPER=es_CR.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=es_CR.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] kableExtra_1.3.1   Rraven_1.0.13      warbleR_1.1.27     NatureSounds_1.0.3 knitr_1.31         seewave_2.1.6      tuneR_1.3.3       

loaded via a namespace (and not attached):
 [1] Rcpp_1.0.6        compiler_4.0.3    shinyBS_0.61      bitops_1.0-6      tools_4.0.3       digest_0.6.27     nlme_3.1-149      lattice_0.20-41  
 [9] evaluate_0.14     lifecycle_0.2.0   viridisLite_0.3.0 mgcv_1.8-33       fftw_1.0-6        rlang_0.4.10      Matrix_1.2-18     rstudioapi_0.11  
[17] yaml_2.2.1        parallel_4.0.3    xfun_0.22         cluster_2.1.0     stringr_1.4.0     httr_1.4.2        xml2_1.3.2        grid_4.0.3       
[25] webshot_0.5.2     glue_1.4.2        R6_2.5.0          dtw_1.22-3        pbapply_1.4-3     soundgen_1.8.2    rmarkdown_2.4     magrittr_2.0.1   
[33] splines_4.0.3     scales_1.1.1      htmltools_0.5.1.1 MASS_7.3-53       rvest_0.3.6       permute_0.9-5     colorspace_1.4-1  stringi_1.5.3    
[41] proxy_0.4-25      signal_0.7-6      RCurl_1.98-1.3    munsell_0.5.0     vegan_2.5-6       rjson_0.2.20