params <- list(EVAL = FALSE) ## ----echo = FALSE, message = FALSE------------------------------------------------------------------------------------------------------------------ # remove all objects rm(list = ls()) # unload all non-based packages out <- sapply(paste('package:', names(sessionInfo()$otherPkgs), sep = ""), function(x) try(detach(x, unload = FALSE, character.only = TRUE), silent = T)) #load packages library(warbleR) library(Rraven) library(knitr) library(kableExtra) options(knitr.table.format = "html") opts_chunk$set(comment = "") opts_knit$set(root.dir = tempdir()) options(width = 150, max.print = 100) #website to fix gifs #https://ezgif.com/optimize ## ----eval = FALSE----------------------------------------------------------------------------------------------------------------------------------- # # download.file( # url = "https://raw.githubusercontent.com/maRce10/Rraven/master/gifs/Rraven.hitgub.html", # destfile = "Rraven.github.html") # ## ----eval = FALSE----------------------------------------------------------------------------------------------------------------------------------- # # remotes::install_github("maRce10/warbleR") # # remotes::install_github("maRce10/Rraven") # # #from CRAN would be # #install.packages("warbleR") # # #load packages # library(warbleR) # library(Rraven) # ## ----eval= F, echo=T-------------------------------------------------------------------------------------------------------------------------------- # # setwd(tempdir()) # # #load example data # data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4", "lbh_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() # ## ----eval= T, echo=F-------------------------------------------------------------------------------------------------------------------------------- #load example data data(list = c("Phae.long1", "Phae.long2", "Phae.long3", "Phae.long4", "lbh_selec_table", "selection_files")) #save sound files in temporary directory writeWave(Phae.long1, file.path(tempdir(), "Phae.long1.wav"), extensible = FALSE) #save sound files writeWave(Phae.long2, file.path(tempdir(), "Phae.long2.wav"), extensible = FALSE) writeWave(Phae.long3, file.path(tempdir(), "Phae.long3.wav"), extensible = FALSE) writeWave(Phae.long4, file.path(tempdir(), "Phae.long4.wav"), extensible = FALSE) #save Raven selection tables in temporary directory out <- lapply(1:4, function(x) writeLines(selection_files[[x]], con = file.path(tempdir(), names(selection_files)[x]))) #providing the name of the column with the sound file names # rvn.dat <- imp_raven(sound.file.col = "Begin.File", all.data = FALSE) #this is the temporary directory location (of course different each time is run) # getwd() ## ----eval=T, echo=T--------------------------------------------------------------------------------------------------------------------------------- list.files(path = tempdir(), pattern = "\\.txt$") ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # # #providing the name of the column with the sound file names # rvn.dat <- imp_raven(all.data = TRUE, path = tempdir()) # # head(rvn.dat) # ## ----eval=TRUE, echo=F, message=F------------------------------------------------------------------------------------------------------------------- #providing the name of the column with the sound file names rvn.dat <- imp_raven(all.data = TRUE, path = tempdir()) kbl <- kable(head(rvn.dat), align = "c", row.names = F, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 11) scroll_box(kbl, width = "808px", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # # rvn.dat <- imp_raven(all.data = TRUE, waveform = TRUE, # path = tempdir()) # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # #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) # ## ----eval=TRUE, echo=FALSE-------------------------------------------------------------------------------------------------------------------------- #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()) kbl <- kable(head(rvn.dat), align = "c", row.names = F, escape = FALSE) kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = TRUE, font_size = 12) # scroll_box(kbl, width = "808", # box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval=FALSE, echo=TRUE-------------------------------------------------------------------------------------------------------------------------- # # # 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) # ## ----eval=TRUE, echo=FALSE-------------------------------------------------------------------------------------------------------------------------- # convert to class selection.table rvn.dat.st <- selection_table(rvn.dat) sp <- spectro_analysis(X = rvn.dat, bp = "frange", wl = 150, pb = FALSE, ovlp = 90, path = tempdir()) kbl <- kable(head(sp), align = "c", row.names = F, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 11) scroll_box(kbl, width = "808px", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval = FALSE----------------------------------------------------------------------------------------------------------------------------------- # # # 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()) # ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # # #remove previous raven data files # unlink(list.files(pattern = "\\.txt$", path = tempdir())) # # #save Raven selection table in the temporary directory # writeLines(selection_files[[5]], con = file.path(tempdir(), # names(selection_files)[5])) # # rvn.dat <- imp_raven(all.data = TRUE, path = tempdir()) # # # Peak freq contour dif length # fcts <- extract_ts(X = rvn.dat, ts.column = "Peak Freq Contour (Hz)") # # head(fcts) # ## ----eval=T, echo=FALSE----------------------------------------------------------------------------------------------------------------------------- #remove previous raven data files unlink(list.files(pattern = "\\.txt$", path = tempdir())) #save Raven selection table in the temporary directory writeLines(selection_files[[5]], con = file.path(tempdir(), names(selection_files)[5])) #save Raven selection table in the temporary directory 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)") kbl <- kable(head(fcts), align = "c", row.names = F, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 11) scroll_box(kbl, width = "808px", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval=F, echo=T--------------------------------------------------------------------------------------------------------------------------------- # # # 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) # ## ----eval=T, echo = F------------------------------------------------------------------------------------------------------------------------------- # Peak freq contour equal length fcts <- extract_ts(X = rvn.dat, ts.column = "Peak Freq Contour (Hz)", equal.length = TRUE) kbl <- kable(head(fcts), align = "c", row.names = F, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 11) scroll_box(kbl, width = "808px", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval=FALSE------------------------------------------------------------------------------------------------------------------------------------- # # # 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) # ## ----eval=TRUE, echo=FALSE-------------------------------------------------------------------------------------------------------------------------- # 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) kbl <- kable(head(fcts), align = "c", row.names = F, escape = FALSE) kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 14) # scroll_box(kbl, width = "900px", # box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval=F, echo=T--------------------------------------------------------------------------------------------------------------------------------- # # freq_DTW(ts.df = fcts, path = tempdir()) # ## ----eval=T, echo=F--------------------------------------------------------------------------------------------------------------------------------- kbl <- kable(freq_DTW(ts.df = fcts, path = tempdir()), align = "c", row.names = T, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = T, font_size = 12) # row_spec(0, angle = 0) scroll_box(kbl, height = "500px", width = "808px", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval = F, echo = T----------------------------------------------------------------------------------------------------------------------------- # # #to simplify the example select a subset of the columns # st1 <- rvn.dat[ ,1:7] # # #check original column names # st1 ## ----eval = T, echo = F----------------------------------------------------------------------------------------------------------------------------- #to simplify the example select a subset of the columns st1 <- rvn.dat[ ,1:7] #check original column names kbl <- kable(st1, align = "c", row.names = F, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 14) ## ----eval = F, echo = T----------------------------------------------------------------------------------------------------------------------------- # # Relabel the basic columns required by warbleR # relabel_colms(st1) # ## ----eval = T, echo = F----------------------------------------------------------------------------------------------------------------------------- rc <- relabel_colms(st1) #check original column names kbl <- kable(rc, align = "c", row.names = F, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 14) ## ----eval = F, echo = T----------------------------------------------------------------------------------------------------------------------------- # # # 2 additional column # relabel_colms(st1, extra.cols.name = "View", # extra.cols.new.name = "Raven view") # ## ----eval = T, echo = F----------------------------------------------------------------------------------------------------------------------------- # plus 2 additional column rc <- relabel_colms(st1, extra.cols.name = "View", "Raven view") kbl <- kable(rc, align = "c", row.names = F, escape = FALSE) kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = FALSE, font_size = 14) ## ----eval=F, echo=T--------------------------------------------------------------------------------------------------------------------------------- # # #create new folder to put cuts # dir.create(file.path(tempdir(), "cuts")) # # # add a rowname column to be able to match cuts and selections # lbh_selec_table$rownames <- sprintf("%02d",1:nrow(lbh_selec_table)) # # # cut files # cut_sels(X = lbh_selec_table, mar = 0.05, path = tempdir(), dest.path = # file.path(tempdir(), "cuts"), # labels = c("rownames", "sound.files", "selec"), pb = FALSE) # # #list cuts # list.files(path = file.path(tempdir(), "cuts")) # ## ----eval=F, echo=T--------------------------------------------------------------------------------------------------------------------------------- # # # Import output (change the name of the file if you used a different one) # xcorr.rav <- imp_corr_mat(file = "BatchCorrOutput.txt", path = tempdir()) # ## ----eval=T, echo=F--------------------------------------------------------------------------------------------------------------------------------- #save Raven selection table in the temporary directory writeLines(selection_files[[6]], con = file.path(tempdir(), names(selection_files)[6])) # Import output (change the name of the file if you used a different one) xcorr.rav <- imp_corr_mat(file = "BatchCorrOutput.txt", path = tempdir()) ## ----eval=F----------------------------------------------------------------------------------------------------------------------------------------- # # xcorr.rav$correlation # ## ----eval=T, echo=F--------------------------------------------------------------------------------------------------------------------------------- kbl <- kable(xcorr.rav$correlation, align = "c", row.names = T, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = T, font_size = 12) # row_spec(0, angle = 0) scroll_box(kbl, height = "500px", width = "808px", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## ----eval=F----------------------------------------------------------------------------------------------------------------------------------------- # xcorr.rav$`lag (s)` # ## ----eval=T, echo=F--------------------------------------------------------------------------------------------------------------------------------- kbl <- kable(xcorr.rav$`lag (s)`, align = "c", row.names = T, escape = FALSE) kbl <- kable_styling(kbl, bootstrap_options = c("striped", "hover", "condensed", "responsive"), full_width = T, font_size = 12) scroll_box(kbl, height = "500px", width = "808px", box_css = "border: 1px solid #ddd; padding: 5px; ", extra_css = NULL) ## --------------------------------------------------------------------------------------------------------------------------------------------------- #convert cross-corr to distance xcorr.rvn <- 1- xcorr.rav$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 <- spectro_analysis(lbh_selec_table, bp = c(1, 11), wl = 150, pb = FALSE, path = tempdir()) #convert them to distance matrix dist.sp.wrblR <- dist(sp.wrblR) vegan::mantel(xcorr.rvn, dist.sp.wrblR) ## ----eval=FALSE, echo=T----------------------------------------------------------------------------------------------------------------------------- # # Select data for a single sound file # st1 <- lbh_selec_table[lbh_selec_table$sound.files == "Phae.long1.wav", ] # # # Export data of a single sound file # exp_raven(st1, file.name = "Phaethornis 1", khz.to.hz = TRUE, path = tempdir()) ## ----eval=FALSE, echo=T----------------------------------------------------------------------------------------------------------------------------- # # Select data for a single sound file # st1 <- lbh_selec_table[lbh_selec_table$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()) # ## ----eval=FALSE, echo=T----------------------------------------------------------------------------------------------------------------------------- # # exp_raven(X = lbh_selec_table, file.name = "Phaethornis multiple sound files", # sound.file.path = tempdir(), single.file = TRUE, path = tempdir()) ## ----eval=FALSE, echo=T----------------------------------------------------------------------------------------------------------------------------- # # 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()) # ## ----eval=FALSE, echo=T----------------------------------------------------------------------------------------------------------------------------- # # detec.res <- raven_batch_detec(raven.path = raven.path, # sound.files = "BlackCappedVireo.aif", # path = file.path(raven.path, "Examples")) # ## ----eval=T, echo=F--------------------------------------------------------------------------------------------------------------------------------- unlink(list.files(pattern = "\\.wav$|\\.txt$", ignore.case = TRUE, path = tempdir())) ## ----session info, echo=F--------------------------------------------------------------------------------------------------------------------------- sessionInfo()