Merge branch 'master' into webpage

.gitignore

@@ -4,3 +4,4 @@
 .httr-oauth
 .DS_Store
 .quarto
+.Rprofile

DESCRIPTION

@@ -1,14 +1,15 @@
 Package: SoundEcology2
 Title: Soundscape Ecology
-Version: 0.0.0.9000
+Version: 0.0.9
 Authors@R: c(
            person(
            "Francisco", "Rivas", 
            email = "frivasfu@purdue.edu", 
            role = c("cre","aut"),
            comment = c(ORCID = "0000-0002-1256-2225")),
            person("Luis", "Villanueva-Rivera", role = "aut"),
-           person("Bryan", "Pijanowski", email = "bpijanow@purdue.edu", role = "aut"))
+           person("Bryan", "Pijanowski", email = "bpijanow@purdue.edu", role = "aut"),
+           person("Angel", "Ramirez", email = "azahramirez@gmail.com", role = "ctb"))
 Description: Computes acoustic indices on audio recordings.
 License: CC BY-NC 4.0
 Encoding: UTF-8
@@ -21,7 +22,6 @@ Imports:
     data.table,
     seewave,
     tuneR,
-    magrittr,
     ineq,
     plotly,
     parallel,
@@ -34,9 +34,15 @@ Imports:
     tibble,
     tidyr,
     tidyverse,
-    vegan,
     viridis,
     stats,
     utils,
-    writexl
+    writexl,
+    grid,
+    future,
+    future.apply
+VignetteBuilder: knitr
+URL: https://github.com/panchorivasf/SoundEcology2
+BugReports: https://github.com/panchorivasf/SoundEcology2/issues 
+Config/testthat/edition: 3
 

NAMESPACE

@@ -3,6 +3,7 @@
 export(aci)
 export(aci_folder)
 export(aci_list)
+export(add_replicate_id)
 export(adi)
 export(adi_folder)
 export(adi_heatmap)
@@ -22,25 +23,33 @@ export(fadi_list)
 export(fci)
 export(fci_folder)
 export(fci_list)
+export(first_recording_hour)
 export(get_fft_params)
 export(harmonize_index)
 export(import_indices)
+export(import_kaleidoscope)
+export(import_kaleidoscope_batch)
 export(import_stereo_mix)
+export(indices_summary)
+export(list_csvs)
 export(list_waves)
 export(merge_index_results)
+export(merge_se2_indices)
 export(nbai)
 export(nbai_folder)
 export(nbai_list)
 export(ndsi)
 export(ndsi_folder)
 export(ndsi_list)
 export(plot_diel_indices)
+export(print_list)
 export(spectral_dynamics)
 export(spectrogram)
 export(spectrogram_3d)
 export(spectrogram_binary)
 export(spectrogram_cutoff)
 export(spectrogram_plotly)
+export(summary_spectrograms)
 export(tai)
 export(tai_folder)
 export(tai_list)
@@ -78,7 +87,11 @@ importFrom(dplyr,summarize)
 importFrom(dplyr,ungroup)
 importFrom(foreach,"%dopar%")
 importFrom(foreach,foreach)
+importFrom(future,multisession)
+importFrom(future,plan)
+importFrom(future.apply,future_lapply)
 importFrom(ggplot2,aes)
+importFrom(ggplot2,annotation_custom)
 importFrom(ggplot2,element_text)
 importFrom(ggplot2,geom_bar)
 importFrom(ggplot2,geom_line)
@@ -88,6 +101,8 @@ importFrom(ggplot2,ggsave)
 importFrom(ggplot2,labs)
 importFrom(ggplot2,scale_x_date)
 importFrom(ggplot2,theme)
+importFrom(grid,gpar)
+importFrom(grid,textGrob)
 importFrom(lubridate,seconds)
 importFrom(magrittr,"%>%")
 importFrom(parallel,detectCores)

R/aci.R

@@ -31,7 +31,9 @@
 #' @import seewave
 #' @import tibble
 #'
-#' @examples aci(tropicalsound)
+#' @examples 
+#' \dontrun{
+#' aci(tropicalsound)}
 aci <- function(wave,
                 freq.res = 50,
                 w.fun = "hanning",
@@ -46,12 +48,10 @@ aci <- function(wave,
   #test arguments
   if (is.na(max.freq)){
     max.freq <- wave@samp.rate / 2
-    # cat(paste("\n max.freq not set, using value of:", max.freq, "\n\n"))
   }
 
   if (is.na(min.freq)){
     min.freq <- 0
-    # cat(paste("\n min.freq not set, using value of:", min.freq, "\n\n"))
   }
 
   if (is.numeric(as.numeric(min.freq))){
@@ -74,14 +74,10 @@ aci <- function(wave,
     stop(" freq.res is not a number.")
   }
 
-
-
-  #Some general values
-  #Get sampling rate
+  # Extract general values
   samplingrate <- wave@samp.rate
   duration <- length(wave@left)/samplingrate
 
-
   if(is.na(j)){
     j <- duration
   }
@@ -188,11 +184,6 @@ aci <- function(wave,
       which_max.freq = dim(specA_left)[1]-1
     }
 
-    # 		cat(which_min.freq)
-    # 		cat(",")
-    # 		cat(which_max.freq)
-    # 		cat(",")
-    # 		cat(dim(specA_left))
     specA_left <- spec_left$amp[which_min.freq:which_max.freq,]
     rm(spec_left)
 
@@ -214,24 +205,13 @@ aci <- function(wave,
 
     rm(left,right)
 
-    # 		specA_rows <- dim(specA_left)[1]
-    # 		specA_cols <- dim(specA_left)[2]
-    #
-    # 		freq_per_row <- specA_rows/nyquist_freq
-    #
-    # 		max_row <- round(max.freq * freq_per_row)
-    #
-    # 		specA_left <- specA_left[1:max_row,]
-    # 		specA_right <- specA_right[1:max_row,]
     specA_rows <- dim(specA_left)[1]
     specA_cols <- dim(specA_left)[2]
 
     fl <- rep(NA, specA_rows)
     delta_fl <- ( max.freq - min.freq ) / specA_rows
     delta_tk <- (length(wave@left)/wave@samp.rate) / specA_cols
 
-    #m <- floor(duration / j)
-    #q <- specA_rows
     no_j <- floor(duration / j)
 
     #Number of values, in each row, for each j period (no. of columns)
@@ -264,7 +244,6 @@ aci <- function(wave,
     }
 
     ACI_tot_left <- sum(ACI_fl_left_vector)
-    # ACI_tot_left <- as.numeric(ACI_tot_left)
 
     #Right channel
     #For each frequency bin fl
@@ -285,31 +264,9 @@ aci <- function(wave,
     }
 
     ACI_tot_right <- sum(ACI_fl_right_vector)
-    # ACI_tot_right <- as.numeric(ACI_tot_right)
-
-    ACI_tot_left_by_min <- round((ACI_tot_left/duration) * 60)#, 2)
-    ACI_tot_right_by_min <- round((ACI_tot_right/duration) * 60)#, 2)
-
-    # cat(paste("  Acoustic Complexity Index (total):\n", "   Left channel: ", sep=""))
-    # cat(ACI_tot_left)
-    # cat(paste("\n", "   Right channel: ", sep=""))
-    # cat(ACI_tot_right)
-    # cat("\n\n")
-    # if (duration > 60){
-    #   cat(paste("  Acoustic Complexity Index (by minute):\n", "   Left channel: ", sep=""))
-    #   cat(ACI_tot_left_by_min)
-    #   cat(paste("\n", "   Right channel: ", sep=""))
-    #   cat(ACI_tot_right_by_min)
-    #   cat("\n\n")
-    # }
-
-    # if(noise.red == 1){
-    #   noise <- "rows"
-    # } else if(noise.red == 2){
-    #   noise <- "columns"
-    # } else {
-      # noise <- "none"
-    # }
+
+    ACI_tot_left_by_min <- round((ACI_tot_left/duration) * 60)
+    ACI_tot_right_by_min <- round((ACI_tot_right/duration) * 60)
 
 
     aciOutputStereo <- tibble(value_l = ACI_tot_left,
@@ -362,7 +319,6 @@ aci <- function(wave,
 
 
     #matrix of values
-    # cat("\n Calculating index. Please wait... \n\n")
     if(noise.red == 1 || noise.red == 2) {
       spec_left <- spectro(left, f = samplingrate, wl = w.len, plot = FALSE,
                            norm = TRUE, dB = NULL, scale = FALSE, wn = w.fun,
@@ -372,7 +328,6 @@ aci <- function(wave,
                            norm = TRUE, dB = NULL, scale = FALSE, wn = w.fun)
     }
 
-    # spec_left <- spectro(left, f = samplingrate, wl = w.len, plot = FALSE, norm = TRUE, dB = NULL, scale = FALSE, wn = w.fun)
 
     specA_left <- spec_left$amp
 
@@ -391,20 +346,13 @@ aci <- function(wave,
     specA_rows <- dim(specA_left)[1]
     specA_cols <- dim(specA_left)[2]
 
-    # 		freq_per_row <- specA_rows/nyquist_freq
-    #
-    # 		max_row <- round(max.freq * freq_per_row)
-    #
-    # 		specA_left <- specA_left[1:max_row,]
-    # 		specA_rows <- dim(specA_left)[1]
 
     fl <- rep(NA, specA_rows)
     delta_fl <- ( max.freq - min.freq ) / specA_rows
     delta_tk <- (length(wave@left)/wave@samp.rate) / specA_cols
 
     no_j <- floor(duration / j)
-    #q <- specA_rows
-    #m <- floor(duration / j)
+
 
     #Number of values, in each row, for each j period (no. of columns)
     I_per_j <- floor(j/delta_tk)
@@ -441,24 +389,6 @@ aci <- function(wave,
     ACI_tot_right <- NA
     ACI_tot_right_by_min <- NA
 
-    # cat("  Acoustic Complexity Index (total): ")
-    # cat(ACI_tot_left)
-    # cat("\n\n")
-    # if (duration > 60){
-    #   cat("  Acoustic Complexity Index (by minute): ")
-    #   cat(ACI_tot_left_by_min)
-    #   cat("\n\n")
-    # }
-
-  # if(noise.red == 1){
-  #   noise <- "rows"
-  # } else if(noise.red == 2){
-  #   noise <- "columns"
-  # } else {
-  #   noise <- "none"
-  # }
-
-
     aciOutputMono <- tibble(value = ACI_tot_left)
 
      # Add metadata columns
@@ -485,10 +415,4 @@ aci <- function(wave,
 
   }
 
-  # invisible(list(AciTotAll_left = ACI_tot_left, AciTotAll_right = ACI_tot_right,
-  #                AciTotAll_left_bymin = ACI_tot_left_by_min, AciTotAll_right_bymin = ACI_tot_right_by_min,
-  #                #AciIfTotAll_left=ACIif_tot_left, AciIfTotAll_right=ACIif_tot_right,
-  #                aci_fl_left_vals = ACI_fl_left_vector, aci_fl_right_vals = ACI_fl_right_vector,
-  #                #aci_if_left_vals=ACI_if_left_vector, aci_if_right_vals=ACI_if_right_vector,
-  #                aci_left_matrix = ACI_left_matrix, aci_right_matrix = ACI_right_matrix))
 }

R/aci_folder.R

@@ -31,7 +31,7 @@
 #' @examples
 #' aci_folder(path/to/folder)
 
-aci_folder <- function (folder,
+aci_folder <- function (folder = NULL,
                        save.csv = TRUE,
                        csv.name = "aci_results.csv",
                        freq.res = 50,
@@ -91,7 +91,7 @@ aci_folder <- function (folder,
                   args_list$noise.red,
                   args_list$rm.offset))
 
-  tibble(file_name = "filename") %>% bind_cols(aci1)
+  tibble(file_name = "filename")  |>  bind_cols(aci1)
 
   # Assess how long it takes to parse 1 file
   timePerFile <-  Sys.time() - startTime
@@ -158,7 +158,7 @@ aci_folder <- function (folder,
                                 args_list$rm.offset)
 
                        # Combine the results for each file into a single row
-                       tibble(file_name = file) %>%
+                       tibble(file_name = file)  |> 
                          bind_cols(aci)
 
 
@@ -172,6 +172,7 @@ aci_folder <- function (folder,
   stopCluster(cl)
 
   if(save.csv == TRUE){
+    resultsWithMetadata$datetime <- format(resultsWithMetadata$datetime, "%Y-%m-%d %H:%M:%S")
     write.csv(resultsWithMetadata, csv.name, row.names = FALSE)
   }
 

R/add_replicate_id.R

@@ -0,0 +1,15 @@
+#' Add replicate id for a dataset with severall treatments 
+#'
+#' @param data a data frame 
+#' @param treatment the name of the column containing the treatment identifiers
+#'
+#' @return a data frame with treatment_id column
+#' @export
+#'
+#' @examples add_replicate_id(my_dataset, treatment = 'zone')
+add_replicate_id <- function(data, treatment = "treatment") {
+  data %>%
+    group_by(treatment) %>%
+    mutate(replicate = dense_rank(sensor_id)) %>%
+    ungroup()
+}