RC

DESCRIPTION

@@ -1,11 +1,11 @@
 Package: tdsc
 Title: Time Domain Signal Coding
-Version: 1.0.2
+Version: 1.0.3
 Authors@R: person("Ed", "Baker", email = "ed@ebaker.me.uk", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-5887-9543"))
 Description: Functions for performing time domain signal coding as used in Chesmore (2001) <doi:10.1016/S0003-682X(01)00009-3>, and related tasks. This package creates the standard S-matrix and A-matrix (with variable lag), has tools to convert coding matrices into distributed matrices, provides published codebooks and allows for extraction of code sequences.
 Depends: R (>= 3.5.0)
 License: GPL-3
-Language: en-UK
+Language: en-GB
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 6.1.1

NEWS.md

@@ -1,4 +1,7 @@
+# tdsc 1.0.3
+*   Allow passing of arguments to plotting functions via tdsc.plot
+
 # tdsc 1.0.2
 *   New wrapper functions compatible with sonicscrewdriver windowing
 *   Helper functionality for plotting A matrices
-*   Added a `NEWS.md` file to track changes to the package.
+*   Added a `NEWS.md` file to track changes to the package.

R/followingCodes.R

@@ -1,13 +1,14 @@
 #' Following Codes
-#' 
+#'
 #' Identifies sequences of codes that follow each other from time domain signal analysis, and optionally plots them as a Sankey diagram.
-#' 
+#'
 #' @param tdsc A TDSC object
 #' @param depth The length of the sequence of codes to search for
 #' @param min_code The minimum value of code to include in sequence
 #' @param max_code The maximum value of code to include in sequence
 #' @param colourCode If plot is alluvial, colour all codes following this code
 #' @param plot If "alluvial" plots the found sequences in a river plot
+#' @param ... Arguments to pass to the plotting function
 #' @keywords TDSC
 #' @export
 #' @examples
@@ -18,12 +19,13 @@
 #' followingCodes(t)
 #' followingCodes(t, colourCode=2,plot="alluvial")
 #' }
-followingCodes <- function (tdsc, 
-                             depth=2, 
-                             min_code=0, 
+followingCodes <- function (tdsc,
+                             depth=2,
+                             min_code=0,
                              max_code=10,
                              colourCode=1,
-                             plot=F) {
+                             plot=F,
+                             ...) {
   codelist <- tdsc@codelist
   fs <- c()
   p <- cbind(min_code:max_code)
@@ -46,10 +48,10 @@ followingCodes <- function (tdsc,
       }
     }
     p <- p_found
-    
+
   }
   colnames(fs) <- c(paste0(rep("Code", depth+1), 1:(depth+1)), "Freq")
-  
+
   if (plot=="alluvial") {
     if (!requireNamespace("alluvial", quietly=TRUE)) {
       stop()
@@ -58,8 +60,9 @@ followingCodes <- function (tdsc,
     alluvial::alluvial( f[,1:(depth+1)], freq=f$Freq, border=NA,
                         hide = f$Freq < stats::quantile(f$Freq, .50),
                         col=ifelse( f$Code1 == colourCode,
-                                    "red", "grey") 
+                                    "red", "grey"),
+                        ...
     )
   }
   return(fs)
-}
+}

R/plot.R

@@ -4,6 +4,7 @@
 #'
 #' @param td A TDSC object
 #' @param plotter Function used to plot the A matrix (persp or perp3D)  or S matrix (hist)
+#' @param ... Parameters to pass to plotting function
 #' @export
 #' @examples
 #' \dontrun{
@@ -14,36 +15,40 @@
 #'
 tdsc.plot <- function(
    td,
-   plotter="persp"
+   plotter="persp",
+   ...
 ){
   if (plotter=="persp") {
-    plot.a.persp(td)
+    plot.a.persp(td, ...)
   }
   if (plotter=="persp3D") {
-    plot.a.persp3D(td)
+    plot.a.persp3D(td, ...)
   }
   if (plotter=="hist") {
-    plot.s.hist(td)
+    plot.s.hist(td, ...)
   }
 }
 
-plot.a.persp <- function(td) {
+plot.a.persp <- function(td, ...) {
   graphics::persp(td@a_matrix,
                   theta = 30, phi = 20,
-                  xlab="Code", ylab="Lagged Code", zlab=""
+                  xlab="Code", ylab="Lagged Code", zlab="",
+                  ...
                   )
 }
 
-plot.a.persp3D <- function(td) {
+plot.a.persp3D <- function(td, ...) {
   package.installed("GA")
   GA::persp3D(x=1:nrow(td@a_matrix),y=1:ncol(td@a_matrix),z=td@a_matrix,
-                     xlab="Code", ylab="Lagged Code", zlab=""
+                     xlab="Code", ylab="Lagged Code", zlab="",
+                      ...
                      )
 }
 
-plot.s.hist <- function(td) {
+plot.s.hist <- function(td, ...) {
   graphics::hist(td@codelist,
        xlab="Code",
-       main=""
+       main="",
+       ...
        )
 }

R/tdsc.w.R

@@ -1,8 +1,8 @@
-#' TDSC analysis comaptible with windowing
+#' TDSC analysis compatible with windowing
 #'
-#' Wrapper function for TDSC analysis that is compatable with the windowing function
+#' Wrapper function for TDSC analysis that is compatible with the windowing function
 #' of the package sonicscrewdriver.
-#' 
+#'
 #' @rdname tdsc.w
 #' @param start Start position in samples
 #' @param wave Wave object to analyse

cran-comments.md

@@ -5,6 +5,4 @@
 
 ## R CMD check results
 
-0 errors | 0 warnings | 1 note
-
-*   This is a new release.
+0 errors | 0 warnings | 0 notes

inst/WORDLIST

@@ -0,0 +1,8 @@
+Bioacoustic
+Chesmore
+Codacy
+doi
+Orthoptera
+perp
+persp
+sonicscrewdriver