Convert S4 methods to S3 and remove plot() function

DESCRIPTION

@@ -10,10 +10,6 @@ License: GPL (>= 3)
 URL: https://archaeostat.github.io/archaeocal/
 BugReports: https://github.com/ArchaeoStat/ArchaeoCal/issues
 Imports: 
-    arkhe (>= 1.9.0),
-    graphics,
-    grDevices,
-    methods,
     utils,
     V8
 Suggests: 
@@ -25,19 +21,3 @@ VignetteBuilder:
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
 RoxygenNote: 7.3.2
-Collate: 
-    'AllClasses.R'
-    'AllGenerics.R'
-    'ArchaeoCal-internal.R'
-    'ArchaeoCal-package.R'
-    'coerce.R'
-    'mutators.R'
-    'oxcal_calibrate.R'
-    'oxcal_configure.R'
-    'oxcal_execute.R'
-    'oxcal_install.R'
-    'oxcal_parse.R'
-    'plot.R'
-    'show.R'
-    'validate.R'
-    'zzz.R'

NAMESPACE

@@ -1,16 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
-S3method(as.data.frame,OxCalOutput)
-S3method(plot,OxCalOutput)
+S3method(as.data.frame,OxCalResults)
+S3method(oxcal_parse,OxCalOutput)
+S3method(oxcal_parse,character)
 export(oxcal_calibrate)
 export(oxcal_configure)
 export(oxcal_execute)
 export(oxcal_install)
-exportMethods(oxcal_parse)
-exportMethods(plot)
-import(arkhe)
-importFrom(methods,.valueClassTest)
-importFrom(methods,new)
-importFrom(methods,setGeneric)
-importFrom(methods,setMethod)
-importFrom(methods,setValidity)
+export(oxcal_parse)

R/ArchaeoCal-internal.R

@@ -1 +1,24 @@
 # HELPERS
+
+#' Default value for NULL
+#'
+#' Replaces `NULL` with a default value.
+#' @param x,y An object.
+#' @return If `x` is `NULL`, returns `y`; otherwise returns `x`.
+#' @keywords internal
+#' @noRd
+`%||%` <- function(x, y) {
+  if (is.null(x)) y else x
+}
+
+# Reexport from base on newer versions of R to avoid conflict messages
+if (exists("%||%", envir = baseenv())) {
+  `%||%` <- get("%||%", envir = baseenv())
+}
+
+assert_exists <- function(x) {
+  if (length(x) == 1 && !file.exists(x)) {
+    stop(sprintf("Could not find %s.", x), call. = FALSE)
+  }
+  invisible(x)
+}

R/ArchaeoCal-package.R

@@ -28,7 +28,3 @@
 #' @docType package
 #' @keywords internal
 "_PACKAGE"
-
-#' @import arkhe
-#' @importFrom methods new setGeneric setMethod setValidity .valueClassTest
-NULL

R/coerce.R

@@ -1,22 +1,29 @@
 # COERCE
-#' @include AllGenerics.R
-NULL
 
-# @return A [`data.frame`] with the following columns:
-#  \describe{
-#   \item{`name`}{}
-#   \item{`operation`}{}
-#   \item{`type`}{}
-#   \item{`date`}{}
-#   \item{`error`}{}
-#   \item{`agreement`}{}
-#   \item{`convergence`}{}
-#   \item{`likelihood`}{}
-#   \item{`posterior`}{}
-#  }
+#' Coerce to a Data Frame
+#'
+#' @param x A [`list`] returned by [`oxcal_parse()`].
+#' @param row.names A [`character`] vector giving the row names for the data
+#'  frame description, or `NULL`.
+#' @param optional A [`logical`] scalar. If `FALSE` then the names of the
+#'  variables in the data frame are checked to ensure that they are
+#'  syntactically valid variable names and are not duplicated.
+#' @param ... Currently not used.
+#' @return A [`data.frame`] with the following columns:
+#'  \describe{
+#'   \item{`name`}{}
+#'   \item{`operation`}{}
+#'   \item{`type`}{}
+#'   \item{`date`}{}
+#'   \item{`error`}{}
+#'   \item{`agreement`}{}
+#'   \item{`convergence`}{}
+#'   \item{`likelihood`}{}
+#'   \item{`posterior`}{}
+#'  }
 #' @export
-#' @method as.data.frame OxCalOutput
-as.data.frame.OxCalOutput <- function(x, ...) {
+as.data.frame.OxCalResults <- function(x, row.names = NULL,
+                                       optional = FALSE, ...) {
   data.frame(
     name = oxcal_get_names(x),
     operation = oxcal_get_operation(x),
@@ -26,6 +33,8 @@ as.data.frame.OxCalOutput <- function(x, ...) {
     agreement = oxcal_get_agreement(x),
     convergence = oxcal_get_convergence(x),
     likelihood = I(oxcal_density(x, prob = "likelihood")),
-    posterior = I(oxcal_density(x, prob = "posterior"))
+    posterior = I(oxcal_density(x, prob = "posterior")),
+    row.names = row.names,
+    check.names = !optional
   )
 }

R/mutators.R

@@ -1,11 +1,9 @@
 # MUTATORS
-#' @include AllGenerics.R
-NULL
 
 # Helpers ======================================================================
 oxcal_range <- function(x, na.rm = TRUE) {
   r <- vapply(
-    X = x@ocd,
+    X = x$ocd,
     FUN = function(x) {
       start_like <- x$likelihood$start
       start_post <- x$posterior$start
@@ -27,7 +25,7 @@ oxcal_range <- function(x, na.rm = TRUE) {
 oxcal_density <- function(x, prob = c("likelihood", "posterior")) {
   prob <- match.arg(prob, several.ok = FALSE)
   lapply(
-    X = x@ocd[-1],
+    X = x$ocd[-1],
     FUN = function(x, prob) {
       years <- seq.int(
         from = x[[prob]]$start,
@@ -43,41 +41,41 @@ oxcal_density <- function(x, prob = c("likelihood", "posterior")) {
 
 oxcal_get_names <- function(x) {
   vapply(
-    X = x@ocd[-1],
+    X = x$ocd[-1],
     FUN = function(x) x$name %||% NA_character_,
     FUN.VALUE = character(1)
   )
 }
 oxcal_get_operation <- function(x) {
-  vapply(X = x@ocd[-1], FUN = `[[`, FUN.VALUE = character(1), i = "op")
+  vapply(X = x$ocd[-1], FUN = `[[`, FUN.VALUE = character(1), i = "op")
 }
 oxcal_get_type <- function(x) {
-  vapply(X = x@ocd[-1], FUN = `[[`, FUN.VALUE = character(1), i = "type")
+  vapply(X = x$ocd[-1], FUN = `[[`, FUN.VALUE = character(1), i = "type")
 }
 oxcal_get_bp_date <- function(x) {
   vapply(
-    X = x@ocd[-1],
+    X = x$ocd[-1],
     FUN = function(x) x[["date"]] %||% NA_real_,
     FUN.VALUE = numeric(1)
   )
 }
 oxcal_get_bp_error <- function(x) {
   vapply(
-    X = x@ocd[-1],
+    X = x$ocd[-1],
     FUN = function(x) x[["error"]] %||% NA_real_,
     FUN.VALUE = numeric(1)
   )
 }
 oxcal_get_agreement <- function(x) {
   vapply(
-    X = x@ocd[-1],
+    X = x$ocd[-1],
     FUN = function(x) x$posterior$agreement %||% NA_real_,
     FUN.VALUE = numeric(1)
   )
 }
 oxcal_get_convergence <- function(x) {
   vapply(
-    X = x@ocd[-1],
+    X = x$ocd[-1],
     FUN = function(x) x$posterior$convergence %||% NA_real_,
     FUN.VALUE = numeric(1)
   )

R/oxcal_calibrate.R

@@ -7,7 +7,7 @@
 #'  to be calibrated.
 #' @param curve A [`character`] string specifying the calibration curve to be
 #'  used.
-#' @return An [`OxCalOutput-class`] object.
+#' @return A [`list`] with class `OxCalResults` (see [oxcal_parse()]).
 #' @example inst/examples/ex-oxcal-calibrate.R
 #' @author N. Frerebeau
 #' @family OxCal tools

R/oxcal_execute.R

@@ -4,10 +4,14 @@
 #' @param file A [`character`] string naming a file (without extension) to
 #'  write `script` to. Output files will be named after `file` and written to
 #'  the same directory.
+#' @param mcmc A [`character`] string giving the name of the output file for
+#'  the MCMC samples (without extension). It must match the `Name` argument of
+#'  OxCal's [`MCMC_Sample()`](https://intchron.org/tools/oxcalhelp/hlp_commands.html)
+#'  function. Only used if `script` contains the `MCMC_Sample()` command.
 #' @param verbose A [`logical`] scalar: should status updates be displayed?
 #' @param ... Further parameters to be passed to [system2()].
 #' @return
-#'  A list with the following elements:
+#'  A [`list`] with class `OxCalOutput` containing the following elements:
 #'  \describe{
 #'   \item{`oxcal`}{A [`character`] string giving the path to the .oxcal file.}
 #'   \item{`js`}{A [`character`] string giving the path to the .js file.}
@@ -21,7 +25,7 @@
 #' @author N. Frerebeau
 #' @family OxCal tools
 #' @export
-oxcal_execute <- function(script, file = NULL,
+oxcal_execute <- function(script, file = NULL, mcmc = "MCMC_Sample",
                           verbose = getOption("ArchaeoCal.verbose"), ...) {
   ## Construct output path
   if (is.null(file)) {
@@ -43,24 +47,20 @@ oxcal_execute <- function(script, file = NULL,
   out <- oxcal_call(oxcal, ...)
   if (verbose) cat(out)
 
-  output <- list(
-    oxcal = oxcal,
-    js = sprintf("%s.js", file),
-    log = sprintf("%s.log", file),
-    txt = sprintf("%s.txt", file)
-  )
-
-  ## MCMC ?
-  csv <- sprintf("%s.csv", file)
+  ## MCMC?
+  csv <- sprintf("%s.csv", mcmc)
   csv <- if (file.exists(csv)) csv else character(0)
 
   ## Output files
-  list(
-    oxcal = oxcal,
-    js = sprintf("%s.js", file),
-    log = sprintf("%s.log", file),
-    txt = sprintf("%s.txt", file),
-    csv = csv
+  structure(
+    list(
+      oxcal = oxcal,
+      js = assert_exists(sprintf("%s.js", file)),
+      log = assert_exists(sprintf("%s.log", file)),
+      txt = assert_exists(sprintf("%s.txt", file)),
+      csv = csv
+    ),
+    class = "OxCalOutput"
   )
 }