bug seltailor when resuming

NEWS.md

@@ -2,23 +2,23 @@
 
 ===============================================================================================
 
-## warbleR 1.1.15
-### (CRAN release date: )
+### *warbleR 1.1.15*
+#### *(CRAN release date: )*
 
 </br>
 
 #### New functions:
 
-* 'multi_DTW': wrapper on dtw for comparing signals described by multiple contours
+* multi_DTW: wrapper on dtw for comparing signals described by multiple contours
 
 #### Changes and additions:
 
 * 'selection_table` now can take files found in different directories and create extended selection tables
 
 ===============================================================================================
 
-## warbleR 1.1.14
-### (CRAN release date: 2018-06-22)
+### *warbleR 1.1.14*
+#### *(CRAN release date: 2018-06-22)*
 
 </br>
 
@@ -28,8 +28,8 @@
 
 ===============================================================================================
 
-## warbleR 1.1.13
-### (CRAN release date: 2018-05-18)
+### *warbleR 1.1.13*
+#### *(CRAN release date: 2018-05-18)*
 
 </br>
 
@@ -42,11 +42,11 @@
 * 'ts.df' argument in 'seltailor' function to adjust frequency contours
 * 'by.song' argument in 'specreator' to create full song spectrograms with labeled elements
 
-## Bug fixes:
+#### Bug fixes:
 
 * Change "http" to "https" protocol for accessing Xeno-Canto recordings in "querxc"
 
-## New functions:
+#### New functions:
 
 * selection_table: converts data frames into an object of classes 'selection_table' or 'extended_selection_table'
 * generic S3 methods for and 'print', 'cbind' and '[' for  classes 'selection_table' or 'extended_selection_table'
@@ -58,8 +58,8 @@
 
 ===============================================================================================
 
-## warbleR 1.1.12
-### (CRAN release date: 2018-03-13)
+### *warbleR 1.1.12*
+#### *(CRAN release date: 2018-03-13)*
 
 </br> 
 
@@ -73,36 +73,36 @@
 * New arguments in 'specreator' to customize control lines/box around selections 
 * Replace internal "message" functions by "cat" (so warnings are printed in black, no red)
 
-## New functions:
+#### New functions:
 
 * track_harm: track harmonic frequency contour
 * sim_song: simulate songs 
 
 
 ===============================================================================================
 
-## warbleR 1.1.10
-### (CRAN release date: 2018-08-28)
+### *warbleR 1.1.10*
+#### *(CRAN release date: 2018-08-28)/
 
 </br>
 
 #### Changes and additions:
 
 * Example sound files have been moved to the new R package 'NatureSounds' (which is now a dependency)
 
-## Bug fixes:
+#### Bug fixes:
 
 * Problem with multiple tags in 'catalog'
 
-## New functions:
+#### New functions:
 
 * rm_sil: removes silence segments (i.e. segments with very low amplitude values) from wave files
 * consolidate: copies (sound) files scattered in several directories into a single folder
 
 ===============================================================================================
 
-## warbleR 1.1.9
-### (CRAN release date: 2017-11-18)
+### *warbleR 1.1.9*
+#### *(CRAN release date: 2017-11-18)*
 
 </br> 
 
@@ -121,7 +121,7 @@
 * "imp.raven" and "imp.syrinx" now import low and high frequency in kHz (if all.data == FALSE)
 * Mew argument "bp" (bandpass) and "wl" in "sig2noise" function to calculate signal-to-noise ratio within a frequency range
 
-## New functions:
+#### New functions:
 
 * is.selection.table: checks if an object is of class 'selection.table'
 * make.selection.table: creates an object of class 'selection.table'
@@ -133,40 +133,42 @@
 * color_spectro: produces spectrograms in which signals are highlighted with colors
 * exp.raven: exports selection tables to a .txt file that can be opened in Raven
 
-## Bug fixes:
+#### Bug fixes:
 
 * Reading wave files with no stereo slot in "specan" and "checksels"
 
 ===============================================================================================
 
-## warbleR 1.1.8
-### (CRAN release date: 2017-04-26)
+### *warbleR 1.1.8*
+#### *(CRAN release date: 2017-04-26)*
 
-## Bug fixes:
+#### Bug fixes:
 
 * installation in some linux distributions
 
 ===============================================================================================
 
-## warbleR 1.1.7
-### (CRAN release date: 2017-04-24)
+### *warbleR 1.1.7*
+#### *(CRAN release date: 2017-04-24)*
 
 </br> 
 
 #### Changes and additions:
 
 * "seltailor" function now can use external graphic devices (X11 or quartz)
 
-## Bug fixes:
+#### Bug fixes:
 
 * installation in windows OS fixed (pbmcapply conflict in previous version)
 
 ===============================================================================================
 
-## warbleR 1.1.6 
-### (CRAN release date: 2017-04-05)
+### *warbleR 1.1.6* 
+#### *(CRAN release date: 2017-04-05)*
+
+</br>
 
-## New functions:
+#### New functions:
 
 * catalog: create song catalogs (i.e. images with multiple spectrograms in several rows/columns that can be color-labeled)
 * catalog2pdf: convert several catalog jpeg's images into single pdf files
@@ -203,16 +205,16 @@ different individuals) would be subset to A-B-A-B-A-B
 * 3 different options (formulas) for calculating signal-to-noise ratio are now available (sig2noise function). In addition the "eq.dur" argument allows to measure a noise segment of the same duration than the signal
 * grid can be removed from spectrograms in compare.methods function
 
-## Bug fixes:
+#### Bug fixes:
 
 * error produced when calculating frequency limits based on dominant frequency contours in xcorr (when frange is not provided)
 * error for identifying readable sound files in some specific .wav formats in checkwavs function
 * error when comparing signals with a high duration difference in xcorr
 
 ===============================================================================================
 
-## warbleR 1.1.5 
-### (CRAN release date: 2017-01-19)
+### *warbleR 1.1.5* 
+#### *(CRAN release date: 2017-01-19)*
 
 </br> 
 
@@ -226,15 +228,15 @@ different individuals) would be subset to A-B-A-B-A-B
 * added 'clip.edges' argument to dfts/ ffts/ dfDTW/ ffDTW/sp.en.ts functions to remove missing values at the start or end of signals
 * more detailed checksels output (now including, sampling rate, duration, number of samples and bits)
 
-## New functions:
+#### New functions:
 
 *  sp.en.ts: extracts the spectral entropy across signals as a time series iteratively
 
 
 ===============================================================================================
 
-## warbleR 1.1.4 
-### (CRAN release date: 2016-11-14)
+### *warbleR 1.1.4* 
+#### *(CRAN release date: 2016-11-14)*
 
 </br> 
 
@@ -245,14 +247,14 @@ different individuals) would be subset to A-B-A-B-A-B
 * new "sp" argument in compare.methods to allow users to input their own spectral parameters
 * new "custom.contour" argument in trackfreqs to allow users to input their own frequency contours 
 
-## Bug fixes:
+#### Bug fixes:
 
 * bug fix for setting 'path' argument in several functions
 * bug fix to due to missing values (undetected) in amplitude detection in trackfreqs, ffts, dfts, ffDTW, and dfDTW  
 
-## New functions:
+#### New functions:
 
 *  filtersels: subsets selection data frames based on manually filtered image files
 *  lspec2pdf: combines lspec images to single pdf files iteratively
 
-
+</br>

R/checksels.R

@@ -100,7 +100,7 @@ checksels <- function(X = NULL, parallel =  1, path = NULL, check.header = FALSE
   #if there are NAs in start or end stop
   if (any(is.na(c(X$end, X$start)))) stop("NAs found in start and/or end")  
 
-  if (any(duplicated(paste(X$sound.files, X$selec)))) stop("Duplicated selection labels for one or more sound files")
+  if (any(duplicated(X[, c("sound.files", "selec")]))) stop("Duplicated selection labels for one or more sound files")
 
   #if any start higher than end stop
   if (any(X$end - X$start < 0)) stop(paste("The start is higher than the end in", length(which(X$end - X$start < 0)), "case(s)"))  
@@ -116,15 +116,10 @@ checksels <- function(X = NULL, parallel =  1, path = NULL, check.header = FALSE
     }}
 
   #check if files are in working directory
-  files <- file.exists(as.character(X$sound.files))
+  files <- file.exists(as.character(unique(X$sound.files)))
   if (all(!files)) 
     stop("no .wav files found")
 
-
-  #if any selection labels are repeated within a sound file
-  if (length(unique(paste(X$sound.files, X$selec))) != nrow(X))
-    stop("Repeated selection labels within (a) sound file(s)")  
-
   # update to new frequency range column names
   if (any(grepl("low.freq|high.freq", names(X)))) { 
     names(X)[names(X) == "low.freq"] <- "bottom.freq"
@@ -134,8 +129,9 @@ checksels <- function(X = NULL, parallel =  1, path = NULL, check.header = FALSE
   #check frequency range columns
   if ("top.freq" %in% colnames(X)) 
   {
+    frq.rng <- X$top.freq - X$bottom.freq
     #if any start higher than end stop
-    if (any(X$top.freq - X$bottom.freq < 0)) stop(paste("The bottom frequency is higher than the top frequency in", length(which(X$top.freq - X$bottom.freq < 0)), "case(s)"))  
+    if (any(frq.rng < 0)) stop(paste("The bottom frequency is higher than the top frequency in", length(which(frq.rng < 0)), "case(s)"))  
     if (any(X$bottom.freq < 0)) stop("bottom frequency lower than 0 for some selections")  
   }    
 
@@ -205,6 +201,7 @@ checksels <- function(X = NULL, parallel =  1, path = NULL, check.header = FALSE
         Y$sample.rate <- NA
         Y$channels <- NA
         Y$bits <- NA
+        Y$sound.file.samples <- NA
       }    } else {
         Y$check.res <- "sound file not found"
         Y$duration <- NA

R/seltailor.R

@@ -238,9 +238,13 @@ seltailor <- function(X = NULL, wl = 512, flim = c(0,22), wn = "hanning", mar =
     cat("all selections have been analyzed")
     stop() 
   }
-  ncl <- intersect(names(ts.df2), names(X))
+
+  if(!is.null(ts.df))
+  {
+    ncl <- intersect(names(ts.df2), names(X))
   ncl <- ncl[!ncl %in% c("sound.files", "selec")]
   }
+  }
 
   dn <- 1:nrow(X)
   if (any(!is.na(X$tailored))) if (length(which(X$tailored == "y")) > 0)