update documentation for S4 classes

proper documentation in Roxygen 4.0 style

NAMESPACE

@@ -21,3 +21,15 @@ export(is.ratio)
 export(ratio)
 export(register_standard)
 export(use_permil)
+exportMethods(as.abundance)
+exportMethods(as.alpha)
+exportMethods(as.delta)
+exportMethods(as.epsilon)
+exportMethods(as.ratio)
+exportMethods(as.value)
+exportMethods(as.weight)
+exportMethods(as.weighted_value)
+exportMethods(fractionate)
+exportMethods(mass_balance)
+exportMethods(shift_reference)
+exportMethods(weight)

R/attribs.R

@@ -87,14 +87,20 @@ setMethod("update_iso", "Intensity", function(obj, attribs) {
 #' @param iso - object to get weight or add weight
 #' @param weight - vector of weight values, has to be a single value or the same length
 #' as the data stored in the isotope value object.
-#' @export
 #' @note This can also be achieved when first initializing (or updating) an object 
 #' via calls to \code{\link{ratio}}, \code{\link{abundance}}, \code{\link{delta}}, etc.
 #' @examples
 #' r <- ratio(0.2)
 #' r <- weight(r, 10)
 #' print(as.weight(r)) # returns 10
+#' @method weight
+#' @export
 setGeneric("weight", function(iso, weight) standardGeneric("weight"))
+
+#' @method weight
+#' @export
+setMethod("weight", "ANY", function(iso, weight) stop("weight not defined for objects of class ", class(iso)))
+
 setMethod("weight", signature("Isoval", "numeric"), function(iso, weight) {
     iso <- update_iso(iso, list(weight = weight))
     validObject(iso) 
@@ -115,8 +121,13 @@ setMethod("weight", signature("Isoval", "numeric"), function(iso, weight) {
 #' frame but keep the isotope values intact, use \code{\link{as.data.frame}} instead.
 #' @seealso \code{\link{as.data.frame}}, \code{\link[base]{as.data.frame}} (base method)
 #' @family data type conversions
+#' @method as.value
 #' @export
 setGeneric("as.value", function(iso) standardGeneric("as.value"))
+
+#' @method as.value
+#' @export
+setMethod("as.value", "ANY", function(iso) stop("as.value not defined for objects of class ", class(iso)))
 setMethod("as.value", "Isoval", function(iso) [email protected])
 setMethod("as.value", "Isosys", function(iso) {
     data.frame(lapply(iso,
@@ -136,8 +147,13 @@ setMethod("as.value", "Isosys", function(iso) {
 #' objects replaced with their weight values. 
 #' @seealso \code{\link{as.data.frame}}, \code{\link[base]{as.data.frame}} (base method)
 #' @family data type conversions
+#' @method as.weight
 #' @export
 setGeneric("as.weight", function(iso) standardGeneric("as.weight"))
+
+#' @method as.weight
+#' @export
+setMethod("as.weight", "ANY", function(iso) stop("as.weight not defined for objects of class ", class(iso)))
 setMethod("as.weight", "Isoval", function(iso) iso@weight)
 setMethod("as.weight", "Isosys", function(iso) {
     data.frame(lapply(iso,
@@ -157,8 +173,13 @@ setMethod("as.weight", "Isosys", function(iso) {
 #' objects replaced with their weighted values. 
 #' @seealso \code{\link{as.data.frame}}, \code{\link[base]{as.data.frame}} (base method)
 #' @family data type conversions
+#' @method as.weighted_value
 #' @export
 setGeneric("as.weighted_value", function(iso) standardGeneric("as.weighted_value"))
+
+#' @method as.weighted_value
+#' @export
+setMethod("as.weighted_value", "ANY", function(iso) stop("as.weighted_value not defined for objects of class ", class(iso)))
 setMethod("as.weighted_value", "Isoval", function(iso) as.weight(iso) * as.value(iso))
 setMethod("as.weighted_value", "Isosys", function(iso) {
     data.frame(lapply(iso,

R/conversion.R

@@ -61,8 +61,12 @@ conversion_error <- function(from, to) {
 #' @return isotope \code{\link{ratio}} object if iso can be converted to a \code{\link{ratio}}, an error otherwise
 #' @rdname as.ratio
 #' @family data type conversions
+#' @method as.ratio
 #' @export
 setGeneric("as.ratio", function(iso) standardGeneric("as.ratio"))
+
+#' @method as.ratio
+#' @export
 setMethod("as.ratio", "ANY", function(iso) conversion_error(iso, "isotope ratio"))
 setMethod("as.ratio", "Ratio", function(iso) iso)
 setMethod("as.ratio", "Ratios", function(iso) iso)
@@ -143,8 +147,12 @@ setMethod("as.ratio", "Delta", function(iso) {
 #' @return isotope \code{\link{abundance}} object if iso can be converted to a \code{\link{abundance}}, an error otherwise
 #' @rdname as.abundance
 #' @family data type conversions
+#' @method as.abundance
 #' @export
 setGeneric("as.abundance", function(iso) standardGeneric("as.abundance"))
+
+#' @method as.abundance
+#' @export
 setMethod("as.abundance", "ANY", function(iso) conversion_error(iso, "isotope abundance"))
 setMethod("as.abundance", "Abundance", function(iso) iso)
 setMethod("as.abundance", "Abundances", function(iso) iso)
@@ -187,8 +195,12 @@ setMethod("as.abundance", "Delta", function(iso) {
 #' @return isotope \code{\link{alpha}} object if iso can be converted to a \code{\link{alpha}}, an error otherwise
 #' @rdname as.alpha
 #' @family data type conversions
+#' @method as.alpha
 #' @export
 setGeneric("as.alpha", function(iso1, iso2) standardGeneric("as.alpha"))
+
+#' @method as.alpha
+#' @export
 setMethod("as.alpha", "ANY", function(iso1, iso2) conversion_error(iso1, "alpha value (ratio of ratios)"))
 
 # two ratios to alpha (uses the arithmetic shorthand) 
@@ -217,8 +229,12 @@ setMethod("as.alpha", signature("Epsilon", "Epsilon"), function(iso1, iso2) {
 #' @return isotope \code{\link{epsilon}} object if iso can be converted to an \code{\link{epsilon}}, an error otherwise
 #' @rdname as.epsilon
 #' @family data type conversions
+#' @method as.epsilon
 #' @export
 setGeneric("as.epsilon", function(iso, permil = use_permil()) standardGeneric("as.epsilon"))
+
+#' @method as.epsilon
+#' @export
 setMethod("as.epsilon", "ANY", function(iso, permil = use_permil()) conversion_error(iso, "epsilon value"))
 setMethod("as.epsilon", "Isosys", function(iso, permil = use_permil()) 
     convert_isosys(iso, "Epsilons", function(df) lapply(as.data.frame(df), function(i) as.epsilon(i, permil = permil))))
@@ -255,8 +271,12 @@ setMethod("as.epsilon", signature(iso = "Epsilon"), function(iso, permil = use_p
 #' @return isotope \code{\link{delta}} object if iso can be converted to a \code{\link{delta}}, an error otherwise
 #' @rdname as.delta
 #' @family data type conversions
+#' @method as.delta
 #' @export
 setGeneric("as.delta", function(iso, ref_ratio, permil = use_permil()) standardGeneric("as.delta"))
+
+#' @method as.delta
+#' @export
 setMethod("as.delta", "ANY", function(iso, ref_ratio, permil = use_permil()) conversion_error(iso, "delta value"))
 setMethod("as.delta", signature(iso = "Isosys", ref_ratio = "missing"), function(iso, ref_ratio, permil = use_permil()) {
     convert_isosys(iso, "Deltas", function(df) lapply(as.data.frame(df), function(i) as.delta(i, permil = permil)))

R/operations.R

@@ -11,8 +11,14 @@ NULL
 #' @param exact - whether to calculate mass balance of delta values exactly (default FALSE), 
 #' use exact_mass_balance to set this paramter globally 
 #' @return weighted abundance or delta value object that represents the combination of the parameters
+#' @method mass_balance
 #' @export
 setGeneric("mass_balance", function(iso, iso2, ..., exact = exact_mass_balance()) standardGeneric("mass_balance"))
+
+#' @method mass_balance
+#' @export
+setMethod("mass_balance", "ANY", function(iso, iso2, ..., exact = exact_mass_balance()) stop("mass_balance not defined for objects of class ", class(iso), ", ", class(iso2))) 
+
 setMethod("mass_balance", signature("Abundance", "Abundance"), function(iso, iso2, ..., exact = exact_mass_balance()) {
     # consider implementing a performance optimized version for many additions
     all <- c(list(iso2), list(...))
@@ -47,8 +53,14 @@ setMethod("mass_balance", signature("Deltas", "Deltas"), function(iso, iso2, ...
 #' implemented with an \code{\link{arithmetic}} shorthand. All calculatinos are
 #' only permissible if the fractionation factors and isotope values have matching
 #' attributes.
+#' @method fractionate
 #' @export
 setGeneric("fractionate", function(frac, iso) standardGeneric("fractionate"))
+
+#' @method fractionate
+#' @export
+setMethod("fractionate", "ANY", function(frac, iso) stop("fractionate not defined for objects of class ", class(frac), ", ", class(iso))) 
+
 setMethod("fractionate", signature("Alpha", "Ratio"), function(frac, iso) {
     iso_attribs_check(frac, iso, include = c("isoname", "major"), text = "cannot generate a ratio from a fractionation factor and a ratio")
     if (frac@compound2 != iso@compound)
@@ -90,8 +102,14 @@ setMethod("fractionate", signature("Epsilon", "ANY"), function(frac, iso) fracti
 #' also implemented with an \code{\link{arithmetic}} shorthand. All calculatinos are
 #' only permissible if the fractionation factors and isotope values have matching
 #' attributes.
+#' @method shift_reference
 #' @export
 setGeneric("shift_reference", function(iso, ref) standardGeneric("shift_reference"))
+
+#' @method shift_reference
+#' @export
+setMethod("shift_reference", "ANY", function(iso, ref) stop("shift_reference not defined for objects of class ", class(iso), ", ", class(ref)))
+
 setMethod("shift_reference", signature("Delta", "Delta"), function(iso, ref) {
     a <- as.alpha(iso) # convert value to shift to an alpha value
     fractionate(a, ref) # "fractionte" new reference with this (will automatically make sure everything is correct)