From 77780175aab74de1f400ef52dfca11d4071434c7 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 10:33:06 -0500
Subject: [PATCH 01/12] improved parameter documentation for
 prep_static_ggspectro.

Fixed bug in segmenting for files with durations or crops that are not exact multiples of xLim
---
 DESCRIPTION                  |  4 ++--
 R/prep_static_ggspectro.R    | 40 +++++++++++++++++++++---------------
 R/processSound.R             | 11 +++++-----
 man/prep_static_ggspectro.Rd | 20 +++++++++---------
 4 files changed, 42 insertions(+), 33 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 92554b5..33cb885 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,7 +1,7 @@
 Package: dynaSpec
 Type: Package
 Title: Dynamic Spectrogram Visualizations
-Version: 1.0.2
+Version: 1.0.3
 Date: 2024-02-20
 Description: A set of tools to generate dynamic spectrogram visualizations in video format.
 License: GPL (>= 2)
@@ -13,7 +13,7 @@ URL: https://github.com/maRce10/dynaSpec
 BugReports: https://github.com/maRce10/dynaSpec/issues
 NeedsCompilation: no
 Suggests: parallel, imager, fs
-RoxygenNote: 7.3.1
+RoxygenNote: 7.3.2
 Repository: CRANs
 Language: en-US
 Encoding: UTF-8
diff --git a/R/prep_static_ggspectro.R b/R/prep_static_ggspectro.R
index 1e6db27..75d3762 100644
--- a/R/prep_static_ggspectro.R
+++ b/R/prep_static_ggspectro.R
@@ -13,20 +13,20 @@
 #' colbins=30,ampThresh=0,bgFlood=FALSE,fontAndAxisCol=NULL,optim=NULL,...)
 #'
 #' @param soundFile should work with URLs, full and relative paths; handles .mp3 and .wav
-#' @param destFolder needs to be like "figures/spectrograms/" to be relative to working directory; goes to soundFile folder by default or working directory if soundFile is a URL; can specify "wd" to output to the working directory
-#' @param outFilename if left out, will use input name in output filename
-#' @param savePNG save static spectrograms as PNGs? They will be exported to destFolder
+#' @param destFolder path to directory to save output. Needs to be like "figures/spectrograms/" to be relative to working directory. Default=parent folder of soundFile. Specify "wd" to output to the working directory, gotten from [get_wd()]
+#' @param outFilename name for output PNG. default=NULL will use input name in output filename.
+#' @param savePNG logical; Save static spectrograms as PNGs? They will be exported to destFolder.
 #' @param colPal color palette; one of "viridis","magma","plasma","inferno","cividis" from the \code{\link[viridis]{viridis}} package OR a 2 value vector (e.g. c("white","black")), defining the start and end of a custom color gradient
-#' @param crop subset of recording to include; if crop=NULL, use whole file; if number, interpreted as crop first X.X sec; if c(X1,X2), interpreted as specific time interval in sec
-#' @param xLim is the time limit in seconds for all spectrograms; i.e. page width in seconds for multi-page dynamic spectrograms (defaults to WAV file length, unless file duration >5s). To override the 5s limit, put xLim=Inf.
-#' @param yLim is the frequency limits (y-axis); default is c(0,10) aka 0-10kHz
-#' @param plotLegend include a legend showing amplitude colors?
-#' @param onlyPlotSpec do you want to just plot the spec and leave out the legend, axes, and axis labels?
-#' @param ampTrans amplitude transform for boosting spectrum contrast; defaults to identity (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)
+#' @param crop subset of recording to include; default crop=NULL will use whole file, up to 10 sec; if a number, interpreted as crop first X.X sec; if c(X1,X2), interpreted as trimming out a specific time interval in sec; if crop=FALSE, will not crop at all, even for recordings over 10 sec.
+#' @param xLim the time limit (x-axis width) in seconds for all spectrograms; i.e. page width in seconds for multi-page dynamic spectrograms (defaults to WAV file length, unless file duration >5s). To override the 5s limit, put xLim=Inf or specify the desired spectrogram x-axis limit.
+#' @param yLim the frequency limits (y-axis); default is c(0,10) aka 0-10kHz
+#' @param plotLegend logical; include a legend showing amplitude colors? default=FALSE
+#' @param onlyPlotSpec logical; do you want to just plot the spec and leave out the legend, axes, and axis labels? default= TRUE
+#' @param ampTrans amplitude transform for boosting spectrum contrast; default=1 (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)
 #' @param min_dB the minimum decibel (quietest sound) to include in the spec; defaults to -30 (-40 would include quieter sounds; -20 would cut out all but very loud sounds)
 #' @param filter apply a bandpass filter? Defaults to none (NULL). Expects 'c(0,2)' where sound from 0 to 2kHz would be filtered out
 #' @param bg  background color (defaults to 1st value of chosen palette)
-#' @param wl  window length for the spectrogram (low values= higher temporal res; high values= higher freq. res). Default 512 is a good tradeoff
+#' @param wl  window length for the spectrogram (low values= higher temporal res; high values= higher freq. res). Default 512 is a good tradeoff; human speech would look better at 1024 or higher, giving higher frequency resolution.
 #' @param ovlp how much overlap (as percent) between sliding windows to generate spec? Default 90 looks good, but takes longer
 #' @param wn window name (slight tweaks on algorithm that affect smoothness of output) see \code{\link[seewave]{spectro}}
 #' @param specWidth what width (in inches) would you like to make your PNG output be, if saving a static spec?
@@ -122,13 +122,21 @@ prep_static_ggspectro <-
         destFolder = dirname(tools::file_path_as_absolute(soundFile))
       }
     }
+    destFolder0 <- destFolder
+    #handle relative destFolder path that ends with /, but doesn't start with /
+    if(!fs::is_absolute_path(destFolder0)){
+      destFolder <- fs::path(fs::path_dir(soundFile),destFolder0)
+      fs::dir_create(destFolder)
+      message("Relative destFolder supplied:'",destFolder0,"'. Will save files to soundFile parent dir:\n > ",destFolder)
+    }
+    
     #Put soundFile in working dir if requested
-    if (destFolder == "wd") {
+    if (destFolder0 == "wd") {
       destFolder <- getwd()
     }
     
-    if (!grepl("/$", destFolder)) {
-      destFolder = paste0(destFolder, "/")
+    if (!grepl("/$", destFolder0)) {
+      destFolder = paste0(destFolder0, "/")
     }#if destFolder missing terminal /, add it
     
     if (is.url(soundFile)) {
@@ -160,7 +168,7 @@ prep_static_ggspectro <-
     
     #Handle file naming for spec
     if (is.null(outFilename)) {
-      outFilename = paste0(tools::file_path_sans_ext(basename(soundFile)), ".PNG")
+      outFilename = paste0(tools::file_path_sans_ext(basename(soundFile)), ".png")
     }
     if (!grepl(".png|PNG", outFilename)) {
       outFilename = paste0(outFilename, ".png")
@@ -184,7 +192,7 @@ prep_static_ggspectro <-
     }
     
     #Convert MP3s to WAV
-    if (tools::file_ext(soundFile) == "mp3") {
+    if (tools::file_ext(soundFile) %in% c("mp3","MP3")) {
       print("***Converting mp3 to wav***")
       wav0 <- tuneR::readMP3(soundFile)
     } else{
@@ -204,7 +212,7 @@ prep_static_ggspectro <-
                    xLim = xLim,
                    filter = filter,
                    ampThresh)
-    
+    browser()
     if (length(yLim) == 1) {
       yLim = c(0, yLim)
     }
diff --git a/R/processSound.R b/R/processSound.R
index 3f21d17..9508264 100644
--- a/R/processSound.R
+++ b/R/processSound.R
@@ -98,11 +98,11 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
   timeRemainder <-
     (ceiling(wavDur / xLim[2]) * xLim[2] - wavDur) > 0.001#(wavDur%/%xLim[2]-wavDur/xLim[2]
   #If user wants to have xLim be Infinite (override 5sec max for long files)
-  if(xLim[2] %in% c(Inf,"Inf")){
+  if (xLim[2] %in% c(Inf, "Inf")) {
     wavDur <- max(length(wav@left), length(wav@right)) / wav@samp.rate
     xLim[2] <- wavDur
-  #Else fill out remainders with filler silence
-  }else if (xLim[2] > wavDur | timeRemainder ) {
+    #Else fill out remainders with filler silence
+  } else if (xLim[2] > wavDur | timeRemainder) {
     if (timeRemainder) {
       diffT <- ceiling(wavDur / xLim[2]) * xLim[2] - wavDur
     } else{
@@ -122,7 +122,8 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
     wavDur <- max(length(wav@left), length(wav@right)) / wav@samp.rate
   }
   #Segment wav or make list of 1 if no segmentation
-  segLens <- seq(0, wavDur, xLim[2])
+  #The ceiling code here is to deal with e.g. duration of 29.999 and xLim=10 that would only produce 2 segments
+  segLens <- seq(0, ceiling(wavDur/xLim[2])*xLim[2], xLim[2])
   indx <- 1:(length(segLens) - 1)
   segWavs <-
     lapply(indx, function(i)
@@ -133,7 +134,7 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
         output = "Wave",
         bit = wav0@bit
       ))
-  #browser()
+  
   return(list(
     newWav = wav,
     segWavs = segWavs,
diff --git a/man/prep_static_ggspectro.Rd b/man/prep_static_ggspectro.Rd
index 810e1f1..8692424 100644
--- a/man/prep_static_ggspectro.Rd
+++ b/man/prep_static_ggspectro.Rd
@@ -14,33 +14,33 @@ colbins=30,ampThresh=0,bgFlood=FALSE,fontAndAxisCol=NULL,optim=NULL,...)
 \arguments{
 \item{soundFile}{should work with URLs, full and relative paths; handles .mp3 and .wav}
 
-\item{destFolder}{needs to be like "figures/spectrograms/" to be relative to working directory; goes to soundFile folder by default or working directory if soundFile is a URL; can specify "wd" to output to the working directory}
+\item{destFolder}{path to directory to save output. Needs to be like "figures/spectrograms/" to be relative to working directory. Default=parent folder of soundFile. Specify "wd" to output to the working directory, gotten from [get_wd()]}
 
-\item{outFilename}{if left out, will use input name in output filename}
+\item{outFilename}{name for output PNG. default=NULL will use input name in output filename.}
 
-\item{savePNG}{save static spectrograms as PNGs? They will be exported to destFolder}
+\item{savePNG}{logical; Save static spectrograms as PNGs? They will be exported to destFolder.}
 
 \item{colPal}{color palette; one of "viridis","magma","plasma","inferno","cividis" from the \code{\link[viridis]{viridis}} package OR a 2 value vector (e.g. c("white","black")), defining the start and end of a custom color gradient}
 
-\item{crop}{subset of recording to include; if crop=NULL, use whole file; if number, interpreted as crop first X.X sec; if c(X1,X2), interpreted as specific time interval in sec}
+\item{crop}{subset of recording to include; default crop=NULL will use whole file, up to 10 sec; if a number, interpreted as crop first X.X sec; if c(X1,X2), interpreted as trimming out a specific time interval in sec; if crop=FALSE, will not crop at all, even for recordings over 10 sec.}
 
 \item{bg}{background color (defaults to 1st value of chosen palette)}
 
 \item{filter}{apply a bandpass filter? Defaults to none (NULL). Expects 'c(0,2)' where sound from 0 to 2kHz would be filtered out}
 
-\item{xLim}{is the time limit in seconds for all spectrograms; i.e. page width in seconds for multi-page dynamic spectrograms (defaults to WAV file length, unless file duration >5s). To override the 5s limit, put xLim=Inf.}
+\item{xLim}{the time limit (x-axis width) in seconds for all spectrograms; i.e. page width in seconds for multi-page dynamic spectrograms (defaults to WAV file length, unless file duration >5s). To override the 5s limit, put xLim=Inf or specify the desired spectrogram x-axis limit.}
 
-\item{yLim}{is the frequency limits (y-axis); default is c(0,10) aka 0-10kHz}
+\item{yLim}{the frequency limits (y-axis); default is c(0,10) aka 0-10kHz}
 
-\item{plotLegend}{include a legend showing amplitude colors?}
+\item{plotLegend}{logical; include a legend showing amplitude colors? default=FALSE}
 
-\item{onlyPlotSpec}{do you want to just plot the spec and leave out the legend, axes, and axis labels?}
+\item{onlyPlotSpec}{logical; do you want to just plot the spec and leave out the legend, axes, and axis labels? default= TRUE}
 
-\item{ampTrans}{amplitude transform for boosting spectrum contrast; defaults to identity (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)}
+\item{ampTrans}{amplitude transform for boosting spectrum contrast; default=1 (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)}
 
 \item{min_dB}{the minimum decibel (quietest sound) to include in the spec; defaults to -30 (-40 would include quieter sounds; -20 would cut out all but very loud sounds)}
 
-\item{wl}{window length for the spectrogram (low values= higher temporal res; high values= higher freq. res). Default 512 is a good tradeoff}
+\item{wl}{window length for the spectrogram (low values= higher temporal res; high values= higher freq. res). Default 512 is a good tradeoff; human speech would look better at 1024 or higher, giving higher frequency resolution.}
 
 \item{ovlp}{how much overlap (as percent) between sliding windows to generate spec? Default 90 looks good, but takes longer}
 

From 61252babc5aab16a6fdc5a7fcf2fdb04d3f74823 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 11:25:13 -0500
Subject: [PATCH 02/12] added title parameter for specs. Updated examples in
 prep_static_ggspectro

---
 R/ggSpec.R                   |  9 ++++++---
 R/prep_static_ggspectro.R    | 17 +++++++++++------
 R/processSound.R             |  2 +-
 man/prep_static_ggspectro.Rd | 15 ++++++++++-----
 4 files changed, 28 insertions(+), 15 deletions(-)

diff --git a/R/ggSpec.R b/R/ggSpec.R
index 524c61b..d0157cf 100644
--- a/R/ggSpec.R
+++ b/R/ggSpec.R
@@ -8,6 +8,7 @@ ggSpec <-
            specWidth,
            specHeight,
            destFolder,
+           title,
            ovlp,
            wl,
            wn,
@@ -108,13 +109,15 @@ ggSpec <-
       
       level=NULL #just to shut up the check
       
-      #Plot that thang
-      #      #
+
+# Plot that thang ---------------------------------------------------------
+
       Glist[[i]] <-
         ggplot2::ggplot(df_i, ggplot2::aes(x = time, y = freq, z = amplitude)) +
         ggplot2::xlim(segLens[i], segLens[i + 1]) + ggplot2::ylim(yLim) +
         #Labels
-        ggplot2::labs(x = "Time (s)", y = "Frequency (kHz)", fill = "Amplitude\n(dB)\n") +
+        ggplot2::labs(x = "Time (s)", y = "Frequency (kHz)", fill = "Amplitude\n(dB)\n",
+                      title=title) +
         {
           #Set scale according to viridis or custom color scheme
           if (isViridis) {
diff --git a/R/prep_static_ggspectro.R b/R/prep_static_ggspectro.R
index 75d3762..61776b8 100644
--- a/R/prep_static_ggspectro.R
+++ b/R/prep_static_ggspectro.R
@@ -20,6 +20,7 @@
 #' @param crop subset of recording to include; default crop=NULL will use whole file, up to 10 sec; if a number, interpreted as crop first X.X sec; if c(X1,X2), interpreted as trimming out a specific time interval in sec; if crop=FALSE, will not crop at all, even for recordings over 10 sec.
 #' @param xLim the time limit (x-axis width) in seconds for all spectrograms; i.e. page width in seconds for multi-page dynamic spectrograms (defaults to WAV file length, unless file duration >5s). To override the 5s limit, put xLim=Inf or specify the desired spectrogram x-axis limit.
 #' @param yLim the frequency limits (y-axis); default is c(0,10) aka 0-10kHz
+#' @param title string for title of plots; default=NULL
 #' @param plotLegend logical; include a legend showing amplitude colors? default=FALSE
 #' @param onlyPlotSpec logical; do you want to just plot the spec and leave out the legend, axes, and axis labels? default= TRUE
 #' @param ampTrans amplitude transform for boosting spectrum contrast; default=1 (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)
@@ -72,12 +73,15 @@
 #' maleBarnSwallow<-prep_static_ggspectro(f[2],destFolder="wd",onlyPlotSpec = FALSE,
 #' bgFlood=TRUE,ampTrans=2,min_dB=-40)
 #'
-#' #much stronger, now let's combine them (you need the cowplot package)
+#' #much stronger, now let's combine them 
+#' (you need the patchwork package to use the / operator to stack plots)
+#' library(patchwork)
+#' (femaleBarnSwallow$spec[[1]]+ggplot2::xlim(0,5)) /
+#' (maleBarnSwallow$spec[[1]]+ggplot2::xlim(0,5))  + 
+#' patchwork::plot_annotation(title="Female and Male barn swallow songs",
+#' caption="Female song (top) is much shorter, but similar complexity to males. See: MR Wilkins et al. (2020) Animal Behaviour 168")
 #'
-#' # cowplot::plot_grid(femaleBarnSwallow$spec[[1]]+xlim(0,5)+ggtitle("female barn swallow song"),
-#' # maleBarnSwallow$spec[[1]]+xlim(0,5)+ggtitle("male barn swallow song"),ncol=1,labels="auto")
-#'
-#' # ggsave("M&F_barn_swallow_song_specs.jpeg")
+#' # ggplot2::ggsave("M&F_barn_swallow_song_specs.jpeg",width=11,height=7)
 #'
 #' # see more examples at https://marce10.github.io/dynaSpec/
 #' }
@@ -98,6 +102,7 @@ prep_static_ggspectro <-
            filter = NULL,
            xLim = NULL,
            yLim = c(0, 10),
+           title=NULL,
            plotLegend = FALSE,
            onlyPlotSpec = TRUE,
            ampTrans = 1,
@@ -212,7 +217,6 @@ prep_static_ggspectro <-
                    xLim = xLim,
                    filter = filter,
                    ampThresh)
-    browser()
     if (length(yLim) == 1) {
       yLim = c(0, yLim)
     }
@@ -227,6 +231,7 @@ prep_static_ggspectro <-
         specWidth = specWidth,
         specHeight = specHeight,
         destFolder = destFolder,
+        title = title,
         colPal = colPal,
         isViridis = isViridis,
         crop = crop,
diff --git a/R/processSound.R b/R/processSound.R
index 9508264..6e7cc4f 100644
--- a/R/processSound.R
+++ b/R/processSound.R
@@ -96,7 +96,7 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
   
   #Add silence at the end if (user-supplied) xLim>cropped Duration or xLim doesn't divide into even segments of wave duration
   timeRemainder <-
-    (ceiling(wavDur / xLim[2]) * xLim[2] - wavDur) > 0.001#(wavDur%/%xLim[2]-wavDur/xLim[2]
+    (ceiling(wavDur / xLim[2]) * xLim[2] - wavDur) > 0#(wavDur%/%xLim[2]-wavDur/xLim[2]
   #If user wants to have xLim be Infinite (override 5sec max for long files)
   if (xLim[2] %in% c(Inf, "Inf")) {
     wavDur <- max(length(wav@left), length(wav@right)) / wav@samp.rate
diff --git a/man/prep_static_ggspectro.Rd b/man/prep_static_ggspectro.Rd
index 8692424..f2afb19 100644
--- a/man/prep_static_ggspectro.Rd
+++ b/man/prep_static_ggspectro.Rd
@@ -32,6 +32,8 @@ colbins=30,ampThresh=0,bgFlood=FALSE,fontAndAxisCol=NULL,optim=NULL,...)
 
 \item{yLim}{the frequency limits (y-axis); default is c(0,10) aka 0-10kHz}
 
+\item{title}{string for title of plots; default=NULL}
+
 \item{plotLegend}{logical; include a legend showing amplitude colors? default=FALSE}
 
 \item{onlyPlotSpec}{logical; do you want to just plot the spec and leave out the legend, axes, and axis labels? default= TRUE}
@@ -98,12 +100,15 @@ bgFlood=TRUE)
 maleBarnSwallow<-prep_static_ggspectro(f[2],destFolder="wd",onlyPlotSpec = FALSE,
 bgFlood=TRUE,ampTrans=2,min_dB=-40)
 
-#much stronger, now let's combine them (you need the cowplot package)
-
-# cowplot::plot_grid(femaleBarnSwallow$spec[[1]]+xlim(0,5)+ggtitle("female barn swallow song"),
-# maleBarnSwallow$spec[[1]]+xlim(0,5)+ggtitle("male barn swallow song"),ncol=1,labels="auto")
+#much stronger, now let's combine them 
+(you need the patchwork package to use the / operator to stack plots)
+library(patchwork)
+(femaleBarnSwallow$spec[[1]]+ggplot2::xlim(0,5)) /
+(maleBarnSwallow$spec[[1]]+ggplot2::xlim(0,5))  + 
+patchwork::plot_annotation(title="Female and Male barn swallow songs",
+caption="Female song (top) is much shorter, but similar complexity to males. See: MR Wilkins et al. (2020) Animal Behaviour 168")
 
-# ggsave("M&F_barn_swallow_song_specs.jpeg")
+# ggplot2::ggsave("M&F_barn_swallow_song_specs.jpeg",width=11,height=7)
 
 # see more examples at https://marce10.github.io/dynaSpec/
 }

From e41dfa35f39d6304eedbbb634b751825d2c0a477 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 11:47:12 -0500
Subject: [PATCH 03/12] added title parameter support to paged_spectro

---
 R/paged_spectro.R         | 4 ++--
 R/prep_static_ggspectro.R | 1 +
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/R/paged_spectro.R b/R/paged_spectro.R
index 2e4e059..82b0696 100644
--- a/R/paged_spectro.R
+++ b/R/paged_spectro.R
@@ -129,12 +129,12 @@ for(i in 1:length(specParams$segWavs))
    cursor<-seq(range_i[1],range_i[2],specParams$xLim[2]/framerate)
   played<-data.frame(xmin=cursor,xmax=rep(range_i[2],length(cursor)),ymin=rep(specParams$yLim[1],length(cursor)),ymax=rep(specParams$yLim[2], length(cursor)))
   
-
   #Make ggplot overlay of highlight box on spectrogram
   vidSegment<-{
     ggplot2::ggplot(played)+ggplot2::xlim(range_i)+ggplot2::ylim(specParams$yLim)+
       #Labels
-      ggplot2::labs(x="Time (s)",y="Frequency (kHz)",fill="Amplitude\n(dB)\n")+
+      ggplot2::labs(x="Time (s)",y="Frequency (kHz)",fill="Amplitude\n(dB)\n",
+                    title=specParams$title)+
       ##Animate() seems to shrink font size a bit
       mytheme_lg(specParams$bg)+
       
diff --git a/R/prep_static_ggspectro.R b/R/prep_static_ggspectro.R
index 61776b8..9fe64f7 100644
--- a/R/prep_static_ggspectro.R
+++ b/R/prep_static_ggspectro.R
@@ -270,6 +270,7 @@ prep_static_ggspectro <-
       isViridis = isViridis,
       xLim = prepped$xLim,
       yLim = yLim,
+      title = title,
       plotLegend = plotLegend,
       onlyPlotSpec = onlyPlotSpec,
       ampTrans = ampTrans,

From 04eebee5993c88d63ce80a8ee1fe0f5629b69e19 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 11:49:23 -0500
Subject: [PATCH 04/12] changed delTemps to more scrutable delete_temp_files
 parameter

---
 R/paged_spectro.R | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/R/paged_spectro.R b/R/paged_spectro.R
index 82b0696..64a3779 100644
--- a/R/paged_spectro.R
+++ b/R/paged_spectro.R
@@ -15,7 +15,7 @@
 #' @param vidName expects "FileName", .mp4 not necessary; if not supplied, will be named after the file you used in prep_static_ggspectro()
 #' @param highlightCol default "#4B0C6BFF" (a purple color to match the default viridis 'inferno' palette)
 #' @param highlightAlpha opacity of the highlight box; default is 0.6
-#' @param cursorCol    Color of the leading edge of the highlight box; default "#4B0C6BFF"
+#' @param cursorCol    Color of the leading edge of the highlight box; default "white"
 #' @param delTemps   Default= TRUE, deletes temporary files (specs & WAV files used to create concatenated video)
 #' @param framerate by default, set to 30 (currently this is not supported, as animate doesn't honor the setting)
 #' @return Nothing is returned, though progress and file save locations are output to user. Video should play after rendering.
@@ -58,7 +58,7 @@
 #' # see more examples at https://marce10.github.io/dynaSpec/
 #' }
 
-paged_spectro <-function(specParams,destFolder,vidName,framerate=30,highlightCol="#4B0C6BFF",highlightAlpha=.6,cursorCol="#4B0C6BFF",delTemps=TRUE)
+paged_spectro <-function(specParams,destFolder,vidName,framerate=30,highlightCol="#4B0C6BFF",highlightAlpha=.6,cursorCol="white",delTemps=TRUE)
 {
  xmin<-ymin <- xmax <- ymax <- NULL 
  #This ^^ suppresses note about "no visible binding for global variable ‘xmax’"

From 540b5eec2ce85c3f9c3d7ada05d27f4f3c9d6347 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 11:52:37 -0500
Subject: [PATCH 05/12] changed default cursor to white

---
 R/paged_spectro.R    |  8 +++-----
 man/paged_spectro.Rd | 16 ++++++++++++----
 2 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/R/paged_spectro.R b/R/paged_spectro.R
index 64a3779..c84fc62 100644
--- a/R/paged_spectro.R
+++ b/R/paged_spectro.R
@@ -8,15 +8,13 @@
 #' is defined by the xLim parameter in \code{\link{prep_static_ggspectro}}. You can also output temporary segmented files, if desired.
 #' 
 #' @aliases pagedSpectro pagedSpec
-#' @usage paged_spectro(specParams,destFolder,vidName,framerate=30,highlightCol="#4B0C6BFF",
-#' highlightAlpha=.6,cursorCol="#4B0C6BFF",delTemps=TRUE)
 #' @param specParams an object returned from \code{\link{prep_static_ggspectro}}
 #' @param destFolder destination of output video; this setting overwrites setting from specParams object
 #' @param vidName expects "FileName", .mp4 not necessary; if not supplied, will be named after the file you used in prep_static_ggspectro()
 #' @param highlightCol default "#4B0C6BFF" (a purple color to match the default viridis 'inferno' palette)
 #' @param highlightAlpha opacity of the highlight box; default is 0.6
 #' @param cursorCol    Color of the leading edge of the highlight box; default "white"
-#' @param delTemps   Default= TRUE, deletes temporary files (specs & WAV files used to create concatenated video)
+#' @param delete_temp_files   Default= TRUE, deletes temporary files (specs & WAV files used to create concatenated video)
 #' @param framerate by default, set to 30 (currently this is not supported, as animate doesn't honor the setting)
 #' @return Nothing is returned, though progress and file save locations are output to user. Video should play after rendering.
 #' @seealso \code{\link{prep_static_ggspectro}}
@@ -58,7 +56,7 @@
 #' # see more examples at https://marce10.github.io/dynaSpec/
 #' }
 
-paged_spectro <-function(specParams,destFolder,vidName,framerate=30,highlightCol="#4B0C6BFF",highlightAlpha=.6,cursorCol="white",delTemps=TRUE)
+paged_spectro <-function(specParams,destFolder,vidName,framerate=30,highlightCol="#4B0C6BFF",highlightAlpha=.6,cursorCol="white",delete_temp_files=TRUE)
 {
  xmin<-ymin <- xmax <- ymax <- NULL 
  #This ^^ suppresses note about "no visible binding for global variable ‘xmax’"
@@ -225,7 +223,7 @@ for(i in 1:length(specParams$segWavs))
   cat(paste0("file saved @",vidName))
   system(paste0('open "',vidName,'"'))
   
-  if(delTemps){unlink(tempdir,recursive=TRUE);print(paste0("FYI temporary file directory deleted @ ",tempdir))}
+  if(delete_temp_files){unlink(tempdir,recursive=TRUE);print(paste0("FYI temporary file directory deleted @ ",tempdir))}
 }#end else which passed FFMPEG check
 }#end paged_spectro definition
 
diff --git a/man/paged_spectro.Rd b/man/paged_spectro.Rd
index 765c51a..0336476 100644
--- a/man/paged_spectro.Rd
+++ b/man/paged_spectro.Rd
@@ -6,8 +6,16 @@
 \alias{pagedSpec}
 \title{Make a paged dynamic spectrogram similar to spectral display in Adobe Audition}
 \usage{
-paged_spectro(specParams,destFolder,vidName,framerate=30,highlightCol="#4B0C6BFF",
-highlightAlpha=.6,cursorCol="#4B0C6BFF",delTemps=TRUE)
+paged_spectro(
+  specParams,
+  destFolder,
+  vidName,
+  framerate = 30,
+  highlightCol = "#4B0C6BFF",
+  highlightAlpha = 0.6,
+  cursorCol = "white",
+  delete_temp_files = TRUE
+)
 }
 \arguments{
 \item{specParams}{an object returned from \code{\link{prep_static_ggspectro}}}
@@ -22,9 +30,9 @@ highlightAlpha=.6,cursorCol="#4B0C6BFF",delTemps=TRUE)
 
 \item{highlightAlpha}{opacity of the highlight box; default is 0.6}
 
-\item{cursorCol}{Color of the leading edge of the highlight box; default "#4B0C6BFF"}
+\item{cursorCol}{Color of the leading edge of the highlight box; default "white"}
 
-\item{delTemps}{Default= TRUE, deletes temporary files (specs & WAV files used to create concatenated video)}
+\item{delete_temp_files}{Default= TRUE, deletes temporary files (specs & WAV files used to create concatenated video)}
 }
 \value{
 Nothing is returned, though progress and file save locations are output to user. Video should play after rendering.

From 6efd4939c6caf100801096ee8e748e8264370ea3 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 11:56:07 -0500
Subject: [PATCH 06/12] fix partially matched filename param in writeWave

---
 R/paged_spectro.R | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/R/paged_spectro.R b/R/paged_spectro.R
index c84fc62..20bcc61 100644
--- a/R/paged_spectro.R
+++ b/R/paged_spectro.R
@@ -97,7 +97,7 @@ if(!missing(vidName)){
     outWAV<-lapply(1:length(specParams$segWavs),function(x) {paste0(tempdir,iName0,"_",x,"_.wav")}) 
     invisible(
       lapply(1:length(specParams$segWavs), function(x){fn=outWAV[[x]]
-          tuneR::writeWave(specParams$segWavs[[x]],file=fn)
+          tuneR::writeWave(specParams$segWavs[[x]],filename=fn)
           cat(paste0("\nSaved temp wav segment: ",fn))}))
       }
     

From b99f31e7e9501210a2c034b48f48a5fcf1c50c51 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 11:59:16 -0500
Subject: [PATCH 07/12] changed cat/print to message() calls

---
 R/paged_spectro.R | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/R/paged_spectro.R b/R/paged_spectro.R
index 20bcc61..bae7cba 100644
--- a/R/paged_spectro.R
+++ b/R/paged_spectro.R
@@ -219,11 +219,13 @@ for(i in 1:length(specParams$segWavs))
    
   }
 
-  cat("\n\nAll done!\n")
-  cat(paste0("file saved @",vidName))
+  message("\n\nAll done!\nfile saved @",vidName)
   system(paste0('open "',vidName,'"'))
   
-  if(delete_temp_files){unlink(tempdir,recursive=TRUE);print(paste0("FYI temporary file directory deleted @ ",tempdir))}
+  if(delete_temp_files){
+    unlink(tempdir,recursive=TRUE)
+    message("FYI temporary file directory deleted @ ",tempdir)
+    }
 }#end else which passed FFMPEG check
 }#end paged_spectro definition
 

From b8c631f5265b68309cb421c51ee86c3951c75c03 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 21:58:44 -0500
Subject: [PATCH 08/12] added resample parameter to speed up spectrogram
 generation

---
 R/ggSpec.R                |  12 +++-
 R/prep_static_ggspectro.R |   6 +-
 R/processSound.R          | 128 ++++++++++++++++++++++++--------------
 3 files changed, 96 insertions(+), 50 deletions(-)

diff --git a/R/ggSpec.R b/R/ggSpec.R
index d0157cf..38bb614 100644
--- a/R/ggSpec.R
+++ b/R/ggSpec.R
@@ -3,6 +3,7 @@
 ggSpec <-
   function(wav,
            soundFile,
+           resampleRate,
            segLens,
            savePNG,
            specWidth,
@@ -34,8 +35,7 @@ ggSpec <-
       nSegs = length(segLens) - 1
     }
     
-    
-    # bg="#ebe834"
+      # bg="#ebe834"
     #Font color adapted from https://stackoverflow.com/questions/3942878/how-to-decide-font-color-in-white-or-black-depending-on-background-color
     
     if (is.null(fontAndAxisCol)) {
@@ -57,6 +57,14 @@ ggSpec <-
     # text(1,1,"READABLE?",cex=5,col=contrastFont)
     
     
+       
+  if(!is.null(resampleRate)){
+    wav0 <- wav #backup
+   message("Original wav (",wav0@samp.rate,"samples/sec) data points: ",length(wav0@left))
+    wav <- tuneR::downsample(wav,samp.rate=resampleRate)
+    message("Original wav (",wav@samp.rate,"samples/sec) data points: ",length(wav@left))
+  }
+    
     #Modified from seewave::ggspectro
     #--->
     # norm =FALSE is important for having similar gain across different recordings
diff --git a/R/prep_static_ggspectro.R b/R/prep_static_ggspectro.R
index 9fe64f7..4f8ffd8 100644
--- a/R/prep_static_ggspectro.R
+++ b/R/prep_static_ggspectro.R
@@ -23,6 +23,7 @@
 #' @param title string for title of plots; default=NULL
 #' @param plotLegend logical; include a legend showing amplitude colors? default=FALSE
 #' @param onlyPlotSpec logical; do you want to just plot the spec and leave out the legend, axes, and axis labels? default= TRUE
+#' @param resampleRate a number in Hz to downsample audio for spectrogram only. This will simplify audio data and speed up generation of spectrogram. Passed to [tuneR::downsample()]. Put NULL to keep original sample rate for spectrogram.
 #' @param ampTrans amplitude transform for boosting spectrum contrast; default=1 (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)
 #' @param min_dB the minimum decibel (quietest sound) to include in the spec; defaults to -30 (-40 would include quieter sounds; -20 would cut out all but very loud sounds)
 #' @param filter apply a bandpass filter? Defaults to none (NULL). Expects 'c(0,2)' where sound from 0 to 2kHz would be filtered out
@@ -106,6 +107,7 @@ prep_static_ggspectro <-
            plotLegend = FALSE,
            onlyPlotSpec = TRUE,
            ampTrans = 1,
+           resampleRate = NULL,
            min_dB = -30,
            wl = 512,
            ovlp = 90,
@@ -216,7 +218,8 @@ prep_static_ggspectro <-
                    crop = crop,
                    xLim = xLim,
                    filter = filter,
-                   ampThresh)
+                   ampThresh=ampThresh)
+    
     if (length(yLim) == 1) {
       yLim = c(0, yLim)
     }
@@ -226,6 +229,7 @@ prep_static_ggspectro <-
       ggSpec(
         wav = prepped$newWav,
         soundFile = soundFile,
+        resampleRate = resampleRate,
         segLens = prepped$segLens,
         savePNG = savePNG,
         specWidth = specWidth,
diff --git a/R/processSound.R b/R/processSound.R
index 6e7cc4f..f94aef3 100644
--- a/R/processSound.R
+++ b/R/processSound.R
@@ -1,8 +1,12 @@
 # processSound: filter, crop, and segment wav (internal function)
 
 processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
+ 
+  
   smplRt <- wav0@samp.rate
+  
   fileDur0 <- max(length(wav0@left), length(wav0@right)) / smplRt
+  
   ##Figure out crop & spectrogram temporal window width
   
   #If crop provided as single digit, interpret as first X sec
@@ -39,20 +43,43 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
   
   #crop is set now for all cases
   
+  
+  # Deal with xLim for segmenting wavs --------------------------------------
+  # if xLim not provided, default to smaller of 5sec or wav duration
+  cropped_dur <- crop[2] - crop[1]
+  
+  if (is.null(xLim)) {
+    xLim <- c(0, min(5, cropped_dur))
+    if (xLim[2] == 5) {
+      message("\n*****\nxLim set to 5 sec by default; define to override\n*****\n")
+    }
+  } else{
+    #If xLim provided as single digit, interpret as X sec
+    if (length(xLim) == 1) {
+      xLim <- c(0, xLim)
+    }
+  }
+  
+  #If user wants to have xLim be Infinite (override 5sec max for long files)
+  if (xLim[2] %in% c(Inf, "Inf")) {
+    xLim[2] <- cropped_dur
+  }
+  
+  
   #assign new wave file for use going forward
   #the bit=wav0@bit is REALLY important! Should be standard, but it doesn't work
-  wav <-
-    if (crop[2] == fileDur0) {
-      wav0
-    } else{
-      seewave::cutw(
-        wav0,
-        from = crop[1],
-        to = crop[2],
-        output = "Wave",
-        bit = wav0@bit
-      )
-    }
+  
+  if (crop[2] == fileDur0) {
+    wav <- wav0
+  } else{
+    wav <- seewave::cutw(
+      wav0,
+      from = crop[1],
+      to = crop[2],
+      output = "Wave",
+      bit = wav0@bit
+    )
+  }
   wavDur <- max(length(wav@left), length(wav@right)) / wav@samp.rate
   
   #Apply filters
@@ -79,38 +106,34 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
   
   
   
-  ##Deal with xLim for segmenting wavs
-  # if xLim not provided, default to smaller of 5sec or wav duration
-  
-  if (is.null(xLim)) {
-    xLim <- c(0, min(5, wavDur))
-    if (xLim[2] == 5) {
-      cat("\n*****\nxLim set to 5 sec by default; define to override\n*****\n")
-    }
-  } else{
-    #If xLim provided as single digit, interpret as X sec
-    if (length(xLim) == 1) {
-      xLim <- c(0, xLim)
-    }
-  }
+  # Make wav file match page xlims ------------------------------------------
+  #Given xLim, what is the full length the recording needs to be?
+  max_page_dur <- ceiling(wavDur / xLim[2]) * xLim[2]
   
   #Add silence at the end if (user-supplied) xLim>cropped Duration or xLim doesn't divide into even segments of wave duration
+  
   timeRemainder <-
-    (ceiling(wavDur / xLim[2]) * xLim[2] - wavDur) > 0#(wavDur%/%xLim[2]-wavDur/xLim[2]
-  #If user wants to have xLim be Infinite (override 5sec max for long files)
-  if (xLim[2] %in% c(Inf, "Inf")) {
-    wavDur <- max(length(wav@left), length(wav@right)) / wav@samp.rate
-    xLim[2] <- wavDur
+    (max_page_dur - wavDur)
+  
+  is_timeRemainder <- timeRemainder > 0
+  
+  
+  #If file is longer than max_page_dur, trim it
+  if (wavDur > max_page_dur) {
+    #trim the wav file again to match a multiple of xLim pages
+    wav <- seewave::cutw(
+      wav,
+      from = crop[1],
+      to = max_page_dur,
+      output = "Wave",
+      bit = wav0@bit
+    )
+    
     #Else fill out remainders with filler silence
-  } else if (xLim[2] > wavDur | timeRemainder) {
-    if (timeRemainder) {
-      diffT <- ceiling(wavDur / xLim[2]) * xLim[2] - wavDur
-    } else{
-      diffT <- xLim[2] - wavDur
-    }
+  } else if (is_timeRemainder) {
     fillerWAV <-
       tuneR::silence(
-        duration = diffT,
+        duration = timeRemainder,
         samp.rate = smplRt,
         xunit = "time",
         pcm = T,
@@ -123,7 +146,8 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
   }
   #Segment wav or make list of 1 if no segmentation
   #The ceiling code here is to deal with e.g. duration of 29.999 and xLim=10 that would only produce 2 segments
-  segLens <- seq(0, ceiling(wavDur/xLim[2])*xLim[2], xLim[2])
+  
+  segLens <- seq(0, ceiling(wavDur / xLim[2]) * xLim[2], xLim[2])
   indx <- 1:(length(segLens) - 1)
   segWavs <-
     lapply(indx, function(i)
@@ -134,12 +158,22 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
         output = "Wave",
         bit = wav0@bit
       ))
-  
-  return(list(
-    newWav = wav,
-    segWavs = segWavs,
-    wavDur = wavDur,
-    segLens = segLens,
-    xLim = xLim
-  ))
+  n_pages = length(segWavs)
+  message(
+    "Segmented original file into ",
+    n_pages,
+    " WAV files, each ",
+    diff(xLim),
+    " seconds long."
+  )
+  return(
+    list(
+      newWav = wav,
+      n_pages = n_pages,
+      segWavs = segWavs,
+      wavDur = wavDur,
+      segLens = segLens,
+      xLim = xLim
+    )
+  )
 }#End processSound

From c6b0f5298fef1f2043b248225c06b2e4f9ce71af Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Tue, 17 Sep 2024 22:25:44 -0500
Subject: [PATCH 09/12] made 15000 the default resample rate for making
 spectrograms. Goes faster and shows a bit more realistic spectrograms with
 discernible background

---
 R/prep_static_ggspectro.R    | 4 ++--
 man/prep_static_ggspectro.Rd | 2 ++
 2 files changed, 4 insertions(+), 2 deletions(-)

diff --git a/R/prep_static_ggspectro.R b/R/prep_static_ggspectro.R
index 4f8ffd8..8e966fe 100644
--- a/R/prep_static_ggspectro.R
+++ b/R/prep_static_ggspectro.R
@@ -23,7 +23,7 @@
 #' @param title string for title of plots; default=NULL
 #' @param plotLegend logical; include a legend showing amplitude colors? default=FALSE
 #' @param onlyPlotSpec logical; do you want to just plot the spec and leave out the legend, axes, and axis labels? default= TRUE
-#' @param resampleRate a number in Hz to downsample audio for spectrogram only. This will simplify audio data and speed up generation of spectrogram. Passed to [tuneR::downsample()]. Put NULL to keep original sample rate for spectrogram.
+#' @param resampleRate a number in Hz to downsample audio for spectrogram only. This will simplify audio data and speed up generation of spectrogram. Passed to [tuneR::downsample()]. Default=15000 shaves off a few seconds without losing much quality. Put NULL to keep original sample rate for spectrogram. Audiofile will not be resampled for MP4.
 #' @param ampTrans amplitude transform for boosting spectrum contrast; default=1 (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)
 #' @param min_dB the minimum decibel (quietest sound) to include in the spec; defaults to -30 (-40 would include quieter sounds; -20 would cut out all but very loud sounds)
 #' @param filter apply a bandpass filter? Defaults to none (NULL). Expects 'c(0,2)' where sound from 0 to 2kHz would be filtered out
@@ -107,7 +107,7 @@ prep_static_ggspectro <-
            plotLegend = FALSE,
            onlyPlotSpec = TRUE,
            ampTrans = 1,
-           resampleRate = NULL,
+           resampleRate = 15000,
            min_dB = -30,
            wl = 512,
            ovlp = 90,
diff --git a/man/prep_static_ggspectro.Rd b/man/prep_static_ggspectro.Rd
index f2afb19..f51f130 100644
--- a/man/prep_static_ggspectro.Rd
+++ b/man/prep_static_ggspectro.Rd
@@ -40,6 +40,8 @@ colbins=30,ampThresh=0,bgFlood=FALSE,fontAndAxisCol=NULL,optim=NULL,...)
 
 \item{ampTrans}{amplitude transform for boosting spectrum contrast; default=1 (actual dB values); specify a decimal number for the lambda value of scales::modulus_trans(); 2.5 is a good place to start. (This amplifies your loud values the most, while not increasing background noise much at all)}
 
+\item{resampleRate}{a number in Hz to downsample audio for spectrogram only. This will simplify audio data and speed up generation of spectrogram. Passed to [tuneR::downsample()]. Default=15000 shaves off a few seconds without losing much quality. Put NULL to keep original sample rate for spectrogram. Audiofile will not be resampled for MP4.}
+
 \item{min_dB}{the minimum decibel (quietest sound) to include in the spec; defaults to -30 (-40 would include quieter sounds; -20 would cut out all but very loud sounds)}
 
 \item{wl}{window length for the spectrogram (low values= higher temporal res; high values= higher freq. res). Default 512 is a good tradeoff; human speech would look better at 1024 or higher, giving higher frequency resolution.}

From 8fb361c8fb660576c688c2851a095361af5ed9b7 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Fri, 20 Sep 2024 11:01:22 -0500
Subject: [PATCH 10/12] fixed error where WAV durations slightly longer than
 30sec making a 40sec video

---
 R/prep_static_ggspectro.R | 1 +
 R/processSound.R          | 8 ++++----
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/R/prep_static_ggspectro.R b/R/prep_static_ggspectro.R
index 8e966fe..bf64c85 100644
--- a/R/prep_static_ggspectro.R
+++ b/R/prep_static_ggspectro.R
@@ -269,6 +269,7 @@ prep_static_ggspectro <-
       soundFile = soundFile,
       destFolder = destFolder,
       outFilename = outFilename,
+      n_pages= length(prepped$segWavs),
       crop = crop,
       colPal = colPal,
       isViridis = isViridis,
diff --git a/R/processSound.R b/R/processSound.R
index f94aef3..c276dbd 100644
--- a/R/processSound.R
+++ b/R/processSound.R
@@ -108,9 +108,7 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
   
   # Make wav file match page xlims ------------------------------------------
   #Given xLim, what is the full length the recording needs to be?
-  max_page_dur <- ceiling(wavDur / xLim[2]) * xLim[2]
-  
-  #Add silence at the end if (user-supplied) xLim>cropped Duration or xLim doesn't divide into even segments of wave duration
+  max_page_dur <- ceiling( round(wavDur,digits=2) / xLim[2]) * xLim[2]
   
   timeRemainder <-
     (max_page_dur - wavDur)
@@ -140,10 +138,12 @@ processSound <- function(wav0, filter, ampThresh, crop, xLim, ...) {
         bit = wav@bit
       )
     wav <- tuneR::bind(wav, fillerWAV)
+  }
+  
     #pastew results in intermittent problems! Don't use! bind seems much more dependable
     #seewave::pastew(wave1=fillerWAV,wave2=wav,at="end",output="Wave",join=T,bit=wav0@bit)
     wavDur <- max(length(wav@left), length(wav@right)) / wav@samp.rate
-  }
+  
   #Segment wav or make list of 1 if no segmentation
   #The ceiling code here is to deal with e.g. duration of 29.999 and xLim=10 that would only produce 2 segments
   

From 96b3545bd6c0caabb66b208562d61f65c6e759e7 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Fri, 20 Sep 2024 11:07:15 -0500
Subject: [PATCH 11/12] remove manual usage declaration

---
 R/prep_static_ggspectro.R    |  5 -----
 man/prep_static_ggspectro.Rd | 33 +++++++++++++++++++++++++++++----
 2 files changed, 29 insertions(+), 9 deletions(-)

diff --git a/R/prep_static_ggspectro.R b/R/prep_static_ggspectro.R
index bf64c85..b1ae6e5 100644
--- a/R/prep_static_ggspectro.R
+++ b/R/prep_static_ggspectro.R
@@ -7,11 +7,6 @@
 #'
 #' @aliases prepStaticSpec prepStaticGGspec
 #'
-#' @usage prep_static_ggspectro(soundFile,destFolder,outFilename,savePNG=FALSE,colPal="inferno",
-#' crop=NULL,bg=NULL,filter=NULL,xLim=NULL,yLim=c(0,10),plotLegend=FALSE,onlyPlotSpec=TRUE,
-#' ampTrans=1,min_dB=-30,wl=512, ovlp=90,wn="blackman",specWidth=9,specHeight=3,
-#' colbins=30,ampThresh=0,bgFlood=FALSE,fontAndAxisCol=NULL,optim=NULL,...)
-#'
 #' @param soundFile should work with URLs, full and relative paths; handles .mp3 and .wav
 #' @param destFolder path to directory to save output. Needs to be like "figures/spectrograms/" to be relative to working directory. Default=parent folder of soundFile. Specify "wd" to output to the working directory, gotten from [get_wd()]
 #' @param outFilename name for output PNG. default=NULL will use input name in output filename.
diff --git a/man/prep_static_ggspectro.Rd b/man/prep_static_ggspectro.Rd
index f51f130..ac9f9dd 100644
--- a/man/prep_static_ggspectro.Rd
+++ b/man/prep_static_ggspectro.Rd
@@ -6,10 +6,35 @@
 \alias{prepStaticGGspec}
 \title{Generate ggplot2-based spectrogram(s), which can be passed to paged_spectro}
 \usage{
-prep_static_ggspectro(soundFile,destFolder,outFilename,savePNG=FALSE,colPal="inferno",
-crop=NULL,bg=NULL,filter=NULL,xLim=NULL,yLim=c(0,10),plotLegend=FALSE,onlyPlotSpec=TRUE,
-ampTrans=1,min_dB=-30,wl=512, ovlp=90,wn="blackman",specWidth=9,specHeight=3,
-colbins=30,ampThresh=0,bgFlood=FALSE,fontAndAxisCol=NULL,optim=NULL,...)
+prep_static_ggspectro(
+  soundFile,
+  destFolder,
+  outFilename = NULL,
+  savePNG = FALSE,
+  colPal = "inferno",
+  crop = NULL,
+  bg = NULL,
+  filter = NULL,
+  xLim = NULL,
+  yLim = c(0, 10),
+  title = NULL,
+  plotLegend = FALSE,
+  onlyPlotSpec = TRUE,
+  ampTrans = 1,
+  resampleRate = 15000,
+  min_dB = -30,
+  wl = 512,
+  ovlp = 90,
+  wn = "blackman",
+  specWidth = 9,
+  specHeight = 3,
+  colbins = 30,
+  ampThresh = 0,
+  bgFlood = FALSE,
+  fontAndAxisCol = NULL,
+  optim = NULL,
+  ...
+)
 }
 \arguments{
 \item{soundFile}{should work with URLs, full and relative paths; handles .mp3 and .wav}

From 45678ed4fe3bd1c117d90689b25f448c3e9992d7 Mon Sep 17 00:00:00 2001
From: Matt Wilkins <matt@galacticpolymath.com>
Date: Wed, 25 Sep 2024 15:49:21 -0500
Subject: [PATCH 12/12] version news update

---
 NEWS.md | 7 +++++++
 1 file changed, 7 insertions(+)

diff --git a/NEWS.md b/NEWS.md
index 397fd5a..f613e37 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -1,3 +1,10 @@
+# *dynaSpec 1.0.3*
+
+* Fix logic for crop and xLim in prep_static_ggspectro()
+* Other fixes to have more predictable behavior of exported MP4 videos using "Matt's approach" with paged_spectro()
+* Added title parameter to add a title to both static and subsequent paged spectrogram (MP4)
+* Added resampleRate parameter to prep_static_ggspectro() for control over resolution of spectrogram (and to speed things up)
+
 # *dynaSpec 1.0.1*
 
 * Fix resampling issue when sampling rate of waves != 44.1 kHz