Refactoring of plot method

Drop the t0 argument and instead use the tspan names attribute for x
axis ticks and labels.

R/SEIR.R

@@ -195,9 +195,9 @@ setMethod("recovered",
 ##' @export
 setMethod("plot",
           signature(x = "SEIR"),
-          function(x, t0 = NULL, ...)
+          function(x, ...)
       {
-          callNextMethod(x, t0 = t0, legend = c("S", "E", "I", "R"), ...)
+          callNextMethod(x, legend = c("S", "E", "I", "R"), ...)
       }
 )
 

R/SIR.R

@@ -189,9 +189,9 @@ setMethod("recovered",
 ##' @export
 setMethod("plot",
           signature(x = "SIR"),
-          function(x, t0 = NULL, ...)
+          function(x, ...)
       {
-          callNextMethod(x, t0 = t0, legend = c("S", "I", "R"), ...)
+          callNextMethod(x, legend = c("S", "I", "R"), ...)
       }
 )
 

R/SISe.R

@@ -221,8 +221,8 @@ setMethod("prevalence",
 ##' @export
 setMethod("plot",
           signature(x = "SISe"),
-          function(x, t0 = NULL, ...)
+          function(x, ...)
       {
-          callNextMethod(x, t0 = t0, legend = c("S", "I"), ...)
+          callNextMethod(x, legend = c("S", "I"), ...)
       }
 )

R/SISe3.R

@@ -315,10 +315,9 @@ setMethod("prevalence",
 ##' @export
 setMethod("plot",
           signature(x = "SISe3"),
-          function(x, t0 = NULL, ...)
+          function(x, ...)
       {
           callNextMethod(x,
-                         t0 = t0,
                          legend = expression(S[1], I[1], S[2], I[2], S[3], I[3]),
                          ...)
       }

R/SISe3_sp.R

@@ -325,10 +325,9 @@ setMethod("prevalence",
 ##' @export
 setMethod("plot",
           signature(x = "SISe3_sp"),
-          function(x, t0 = NULL, ...)
+          function(x, ...)
       {
           callNextMethod(x,
-                         t0 = t0,
                          legend = expression(S[1], I[1], S[2], I[2], S[3], I[3]),
                          ...)
       }

R/SISe_sp.R

@@ -232,8 +232,8 @@ setMethod("prevalence",
 ##' @export
 setMethod("plot",
           signature(x = "SISe_sp"),
-          function(x, t0 = NULL, ...)
+          function(x, ...)
       {
-          callNextMethod(x, t0 = t0, legend = c("S", "I"), ...)
+          callNextMethod(x, legend = c("S", "I"), ...)
       }
 )

R/scheduled_events.R

@@ -300,6 +300,8 @@ scheduled_events <- function(E      = NULL,
 ##' @param frame.plot a logical indicating whether a box should be
 ##'     drawn around the plot.
 ##' @param ... additional arguments affecting the plot.
+##' @importFrom graphics plot
+##' @importFrom graphics mtext
 ##' @keywords internal
 plot_scheduled_events <- function(x,
                                   y,
@@ -338,13 +340,14 @@ plot_scheduled_events <- function(x,
     graphics::mtext("Time", side = 1, line = 2)
 }
 
-##' @rdname plot-methods
+##' Plot \code{\linkS4class{scheduled_events}}
+##'
 ##' @param frame.plot Draw a frame around each plot. Default is FALSE.
+##' @name plot-methods
 ##' @aliases plot plot-methods plot,scheduled_events-method
 ##' @docType methods
-##' @importFrom graphics par
 ##' @importFrom graphics plot
-##' @importFrom graphics mtext
+##' @importFrom graphics par
 ##' @importFrom stats xtabs
 ##' @export
 setMethod("plot",

R/siminf_model.R

@@ -418,11 +418,8 @@ setMethod("run",
 ##' Plot \code{\linkS4class{siminf_model}}
 ##'
 ##' @param x The \code{model} to plot
+##' @param y Unused.
 ##' @param legend The character vector to appear in the legend.
-##' @param t0 The first date of \code{x@@tspan} as a character string
-##' in format 'yyyy-mm-dd'. Default is NULL which prints the x-axis
-##' labels as the sequence 1:length(x@@tspan). If non-null, the labels
-##' are converted to dates.
 ##' @param col The plotting color for each compartment. Default is
 ##' black.
 ##' @param lty The line type for each compartment. Default is the
@@ -451,7 +448,7 @@ setMethod("run",
 ##' plot(result)
 setMethod("plot",
           signature(x = "siminf_model"),
-          function(x, legend, t0 = NULL, col = NULL, lty = NULL, ...)
+          function(x, legend, col = NULL, lty = NULL, ...)
       {
           if (identical(dim(x@U), c(0L, 0L)))
               stop("Please run the model first, the 'U' matrix is empty")
@@ -478,31 +475,33 @@ setMethod("plot",
               lty <- seq_len(dim(m)[1])
 
           ## Plot
-          if (is.null(t0)) {
-              plot(m[1,], type = "l", ylab = "Proportion", ylim = c(0, 1),
-                   col = col[1], lty = lty[1], ...)
+          if (is.null(names(x@tspan))) {
+              plot(m[1,], type = "l", ylab = "Proportion",
+                   ylim = c(0, 1), col = col[1], lty = lty[1], ...)
           } else {
-              plot(m[1,], type = "l", ylab = "Proportion", ylim = c(0, 1),
-                   col = col[1], lty = lty[1], xaxt = "n")
-          }
-          title(xlab = "Day", outer = TRUE, line = 0)
-          if (!is.null(t0)) {
-              axis(side = 1, at = seq_len(dim(m)[2]),
-                   labels = as.Date(x@tspan - min(x@tspan),
-                       origin = as.Date(t0)))
+              plot(x = as.Date(names(x@tspan)), y = m[1,], type = "l",
+                   ylab = "Proportion", ylim = c(0, 1), col = col[1],
+                   lty = lty[1], ...)
           }
+          title(xlab = "Time", outer = TRUE, line = 0)
           for (i in seq_len(dim(m)[1])[-1]) {
-              lines(m[i, ], type = "l", lty = lty[i], col = col[i], ...)
+              if (is.null(names(x@tspan))) {
+                  lines(m[i, ], type = "l", lty = lty[i],
+                        col = col[i], ...)
+              } else {
+                  lines(x = as.Date(names(x@tspan)), y = m[i, ],
+                        type = "l", lty = lty[i], col = col[i], ...)
+              }
           }
 
           ## Add legend below plot
           par(fig = c(0, 1, 0, 1),
               oma = c(0, 0, 0, 0),
               mar = c(0, 0, 0, 0), new = TRUE)
           plot(0, 0, type = "n", bty = "n", xaxt = "n", yaxt = "n")
-          graphics::legend("bottom", inset = c(0, 0),
-                           lty = lty, col = col, bty = "n",
-                           horiz = TRUE, legend = legend)
+          graphics::legend("bottom", inset = c(0, 0), lty = lty,
+                           col = col, bty = "n", horiz = TRUE,
+                           legend = legend)
       }
 )
 

tests/SISe3.R

@@ -1506,7 +1506,7 @@ stopifnot(identical(I_observed, I_expected))
 ## Check SISe3 plot method
 pdf_file <- tempfile(fileext = ".pdf")
 pdf(pdf_file)
-plot(result, t0 = "2015-01-01")
+plot(result)
 dev.off()
 stopifnot(file.exists(pdf_file))
 unlink(pdf_file)

tests/SISe3_sp.R

@@ -1629,7 +1629,7 @@ stopifnot(identical(I_observed, I_expected))
 ## Check SISe3_sp plot method
 pdf_file <- tempfile(fileext = ".pdf")
 pdf(pdf_file)
-plot(result, t0 = "2015-01-01")
+plot(result)
 dev.off()
 stopifnot(file.exists(pdf_file))
 unlink(pdf_file)