isotopia update

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: isotopia
 Type: Package
 Title: Work with isotopic data in R
-Version: 0.2
+Version: 0.3
 Date: 2014-04-05
 Author: Sebastian Kopf
 Maintainer: Sebastian Kopf <[email protected]>
 Description: R interface for working with isotopic data (abundances, ratios,
-    delta values, etc.).
+    fractionation factors, delta values, etc.).
 License: GPL-3
 LazyLoad: yes
 Roxygen: list(wrap = FALSE)

R/arithmetic.R

@@ -95,8 +95,7 @@ setMethod("+", signature(e1 = "Abundance", e2 = "Abundance"), function(e1, e2) {
 #' @usage delta +- delta
 #' @details
 #' \code{delta+-delta} is a shorthand for calculating the isotopic mass balance of
-#' two \code{\link{delta}} objects, see \code{\link{mass_balance}} for details,
-#' will use the global \code{\link{exact_mass_balance}} setting for the calculation
+#' two \code{\link{delta}} objects, see \code{\link{mass_balance}} for details
 #' @name arithmetic 
 #' @rdname arithmetic
 NULL
@@ -329,9 +328,9 @@ setMethod("/", signature(e1 = "FractionationFactor", e2 = "FractionationFactor")
 
 #' @usage delta / delta
 #' @details
-#' \code{delta/delta} creates an \code{\link{alpha}} fractionation factor object that
+#' \code{delta/delta} creates an \code{\link{fractionation_factor}} object that
 #' describes the fractionation factor between the two compounds, requires the reference
-#' name of the two delta values to be identical. This is a shorthand for the \link{frac_factor} function.
+#' name of the two delta values to be identical. This is a shorthand for the \link{to_ff} function.
 #' @name arithmetic 
 #' @rdname arithmetic
 NULL

R/attribs.R

@@ -154,23 +154,23 @@ setMethod("weight", signature("Isoval", "numeric"), function(iso, weight) {
 #' primitive data value(s).  
 #' 
 #' @param notation specifiy which notation to return the value in (default is the notation
-#' that hte object is in)
+#' that the object is in)
 #' @return In the case of a single isotope object (Isoval), returns the numeric
-#' vector of raw values stored in the object (same as \code{\link{as.numeric}}). 
+#' vector of raw values stored in the object (same as \code{\link[base]{as.numeric}}). 
 #' In the case of an isotope system (Isosys),
 #' returns the data frame underlying the object with all its isotope value
 #' objects also replaced with their numeric raw values. To just get the data
 #' frame but keep the isotope values intact, use \code{\link{as.data.frame}} instead.
-#' @seealso \code{\link{as.numeric}}, \code{\link{as.data.frame}}, \code{\link[base]{as.data.frame}} (base method)
+#' @seealso \code{\link[base]{as.numeric}}, \code{\link{as.data.frame}}, \code{\link[base]{as.data.frame}} (base method)
 #' @family data type attributes
 #' @method get_value
 #' @export
-setGeneric("get_value", function(iso, notation = "raw") standardGeneric("get_value"))
+setGeneric("get_value", function(iso, notation = iso@notation) standardGeneric("get_value"))
 
 #' @method get_value
 #' @export
-setMethod("get_value", "ANY", function(iso, notation = "raw") stop("get_value not defined for objects of class ", class(iso)))
-setMethod("get_value", "numeric", function(iso, notation = "raw") iso) # allow this for simplicity so this is similiar to as_numeric
+setMethod("get_value", "ANY", function(iso, notation) stop("get_value not defined for objects of class ", class(iso)))
+setMethod("get_value", "numeric", function(iso, notation = NULL) iso) # allow this for simplicity so this is similiar to as_numeric
 setMethod("get_value", "Isoval", function(iso, notation = iso@notation) as.numeric(switch_notation(iso, notation)))
 setMethod("get_value", "Isosys", function(iso, notation = NULL) {
     data.frame(lapply(iso,

R/conversion.R

@@ -137,7 +137,7 @@ setMethod("to_ratio", "Delta", function(iso) {
         else if (length(stds) > 1)
             message("No reference ratio registered with the delta value, tried to find one from the registered standards but found multiple, delta: ", get_label(iso))
         else if (length(stds) == 1) {
-            message("Successfully found a matching standard to convert delta value without registered reference: ", get_label(stds[[1]]), ": ", get_value(stds[[1]]))
+            message("Successfully found a registered standard to convert delta value: ", get_label(stds[[1]]), ": ", signif(get_value(stds[[1]]), 4))
             iso@ref_ratio <- get_value(stds[[1]])
         }
     }
@@ -200,6 +200,7 @@ setMethod("to_abundance", "Intensities", function(iso) to_abundance(to_ratio(iso
 
 # delta to abundance
 setMethod("to_abundance", "Delta", function(iso) {
+    # FIXME: add warning for isotope systems with more than one ratio?
     r <- to_ratio(iso)
     to_abundance(r)
 })
@@ -213,7 +214,7 @@ setMethod("to_abundance", "Delta", function(iso) {
 #' 
 #' @usage to_ff(iso1, iso2)
 #' @details
-#' The \code{frac_factor(...)} function calculates the fractionation factor between two isotope data objects
+#' The \code{to_ff(...)} function calculates the fractionation factor between two isotope data objects
 #' (for example two \code{\link{delta}} values, two \code{\link{ratio}}, or two \code{\link{ff}}).
 #' All calculatinos are only permissible if the isotope values have matching
 #' attributes and fractionation factors will be returend in the default notation
@@ -324,6 +325,12 @@ setMethod("to_delta", signature(iso = "FractionationFactor", ref_ratio = "Ratio"
 
 # ratio to delta =========
 
+# ratio to delta (with numeric ref ratio)
+setMethod("to_delta", signature("Ratio", "missing"), function(iso, ref_ratio) {
+    stop("Can't convert from a ratio to a delta value without a reference ratio.")
+})
+
+
 # ratio to delta (with numeric ref ratio)
 setMethod("to_delta", signature("Ratio", "numeric"), function(iso, ref_ratio) {
     to_delta(iso, update_iso(ratio(ref_ratio), list(isoname = iso@isoname, major = iso@isoname)))

R/initialization.R

@@ -54,12 +54,12 @@ ab <- abundance
 
 #' Fractionation factor
 #' 
-#' FIXME, change description
-#' Generate a fractionation factor (alpha value = ratio of two isotope ratios) object. See \link{isotopia} for general information on initializing
-#' and converting isotope data objects.
-#' Fractionation factors can be easily converted from values in one notation to values in 
+#' Generate a fractionation factor object. Can be initialized in \code{alpha} and
+#' \code{epsilon} notation. Fractionation factors can be easily converted from values in one notation to values in 
 #' another notation by using \code{\link{switch_notation}}.
 #' 
+#' See \link{isotopia} for general information on initializing
+#' and converting to other isotope data objects.
 #' The \code{ff} function is a shorthand for \code{fractionation_factor} but otherwise identical.
 #' 
 #' @param ... - numeric vectors (can be named) to turn into fractionation factors
@@ -90,8 +90,7 @@ ff <- fractionation_factor
 #' another notation by using \code{\link{switch_notation}}.
 #' 
 #' For mass balance calculations with delta values, simply add the appropriate weights (if different from
-#' the default) and use \code{delta(...) + delta(...)}. Use \code{\link{exact_mass_balance}(TRUE/FALSE)}
-#' to adjust how these are calculated.
+#' the default) and use \code{delta(...) + delta(...)}. 
 #' 
 #' @param ... - numeric vectors (can be named) to turn into delta values
 #' @param major - name of the major isotope in the isotope system [optional]

R/operations.R

@@ -9,26 +9,26 @@ NULL
 #' is also implemented with an \code{\link{arithmetic}} shorthand.
 #'
 #' @param ... - any number of weighted isotope value objects (have to be all either abundance or delta)
-#' @param exact - whether to calculate mass balance of delta values exactly (default FALSE), 
-#' use exact_mass_balance to set this paramter globally 
+#' @param exact - whether to calculate mass balance of delta values exactly (default FALSE), not
+#' fully implemented yet
 #' @return weighted abundance or delta value object that represents the combination of the parameters
 #' @family operations
 #' @method mass_balance
 #' @export
-setGeneric("mass_balance", function(iso, iso2, ..., exact = exact_mass_balance()) standardGeneric("mass_balance"))
+setGeneric("mass_balance", function(iso, iso2, ..., exact = get_iso_opts("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", "ANY", function(iso, iso2, ..., exact = get_iso_opts("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()) {
+setMethod("mass_balance", signature("Abundance", "Abundance"), function(iso, iso2, ..., exact = get_iso_opts("exact_mass_balance")) {
     # consider implementing a performance optimized version for many additions
     all <- c(list(iso2), list(...))
     for (i in all)
         iso = iso + i
     iso
 })
-setMethod("mass_balance", signature("Delta", "Delta"), function(iso, iso2, ..., exact = exact_mass_balance()) {
+setMethod("mass_balance", signature("Delta", "Delta"), function(iso, iso2, ..., exact = get_iso_opts("exact_mass_balance")) {
     if (exact)
         stop("not implemented yet!") # should be implemented here rather than in the operators
 
@@ -38,15 +38,15 @@ setMethod("mass_balance", signature("Delta", "Delta"), function(iso, iso2, ...,
     iso
 })
 
-setMethod("mass_balance", signature("Deltas", "Deltas"), function(iso, iso2, ..., exact = exact_mass_balance()) {
+setMethod("mass_balance", signature("Deltas", "Deltas"), function(iso, iso2, ..., exact = get_iso_opts("exact_mass_balance")) {
     stop("not implemented yet")
 })
 
 #' Fractionate an isotopic value
 #' 
-#' This function calculates the outcome of isotopic fractionation by a \code{\link{fractionation_fractor}}
+#' This function calculates the outcome of isotopic fractionation by a \code{\link{fractionation_factor}}
 #' and can be applied to \code{\link{ratio}} data, \code{\link{delta}} values or other
-#' \code{\link{fractionation_fractor}} objects.
+#' \code{\link{fractionation_factor}} objects.
 #' @param frac the fractionation factor \code{\link{ff}} used to fractionate the isotope value
 #' @param iso the isotope object to fractionate
 #' @return an object of the same type as \code{iso}

R/utils.R

@@ -20,7 +20,7 @@ drop_list <- function(l) {
 #' 
 #' This small utility function is just a convenient wrapper for running
 #' isotope calculations silently without outputting any of the warnings or
-#' messages (it uses \link{suppressMessages} and \link{suppressWarnings}
+#' messages (it uses \link[base]{suppressMessages} and \link[base]{suppressWarnings}
 #' internally) that might occur. Use with care to suppress warnings, you
 #' might end up hiding important information.
 #' @export

R/zzz.R

@@ -12,11 +12,11 @@ setLoadActions(function(ns) {
         exact_mass_balance = FALSE
     )
 
-#     suppressWarnings({
-#         register_standard(ratio(`2H` = to_ratio(abundance(0.00015574)), major = "1H", compound = "VSMOW")) # from IUPAC report
-#         register_standard(ratio(`13C` = 0.011237, major = "12C", compound = "VPDB"))
-#         register_standard(ratio(`15N` = 0.003677, major = "14N", compound = "Air"))
-#         register_standard(ratio(`18O` = 0.0020052, major = "16O", compound = "VSMOW"))
-#         register_standard(ratio(`34S` = 0.0045005, major = "32S", compound = "CDT"))
-#     })
+    suppressWarnings({
+        register_standard(ratio(`2H` = to_ratio(abundance(0.00015574)), major = "1H", compound = "VSMOW")) # from IUPAC report
+        register_standard(ratio(`13C` = 0.011237, major = "12C", compound = "VPDB"))
+        register_standard(ratio(`15N` = 0.003677, major = "14N", compound = "Air"))
+        register_standard(ratio(`18O` = 0.0020052, major = "16O", compound = "VSMOW"))
+        register_standard(ratio(`34S` = 0.0045005, major = "32S", compound = "CDT"))
+    })
 })

man/arithmetic.Rd

@@ -38,8 +38,7 @@ have matching attributes (isotope name, major isotope, etc.).
 two \code{\link{abundance}} objects, see \code{\link{mass_balance}} for details
 
 \code{delta+-delta} is a shorthand for calculating the isotopic mass balance of
-two \code{\link{delta}} objects, see \code{\link{mass_balance}} for details,
-will use the global \code{\link{exact_mass_balance}} setting for the calculation
+two \code{\link{delta}} objects, see \code{\link{mass_balance}} for details
 
 \code{alpha - 1} is a shorthand for converting a fractionation factor from
 alpha to epsilon notation. The ff object has to be in alpha notation,
@@ -69,8 +68,8 @@ This is a shorthand for the \link{to_ff} function.
 either the denominator names or numerator names of the two objects are identical (i.e. they "cancel").
 This is a shorthand for the \link{to_ff} function.
 
-\code{delta/delta} creates an \code{\link{alpha}} fractionation factor object that
+\code{delta/delta} creates an \code{\link{fractionation_factor}} object that
 describes the fractionation factor between the two compounds, requires the reference
-name of the two delta values to be identical. This is a shorthand for the \link{frac_factor} function.
+name of the two delta values to be identical. This is a shorthand for the \link{to_ff} function.
 }
 

man/delta.Rd

@@ -35,8 +35,7 @@ another notation by using \code{\link{switch_notation}}.
 }
 \details{
 For mass balance calculations with delta values, simply add the appropriate weights (if different from
-the default) and use \code{delta(...) + delta(...)}. Use \code{\link{exact_mass_balance}(TRUE/FALSE)}
-to adjust how these are calculated.
+the default) and use \code{delta(...) + delta(...)}.
 }
 \examples{
 delta(50, notation = "permil") # enter as permil value

man/fractionate.Rd

@@ -14,9 +14,9 @@ fractionate(frac, iso)
 an object of the same type as \code{iso}
 }
 \description{
-This function calculates the outcome of isotopic fractionation by a \code{\link{fractionation_fractor}}
+This function calculates the outcome of isotopic fractionation by a \code{\link{fractionation_factor}}
 and can be applied to \code{\link{ratio}} data, \code{\link{delta}} values or other
-\code{\link{fractionation_fractor}} objects.
+\code{\link{fractionation_factor}} objects.
 }
 \note{
 Several of these calculations are also

man/fractionation_factor.Rd

@@ -26,13 +26,13 @@ See \code{\link{switch_notation}} on details how to convert between notations.}
 \item{cbot}{- name of the compound representing the bottom isotope ratio [optional]}
 }
 \description{
-FIXME, change description
-Generate a fractionation factor (alpha value = ratio of two isotope ratios) object. See \link{isotopia} for general information on initializing
-and converting isotope data objects.
-Fractionation factors can be easily converted from values in one notation to values in
+Generate a fractionation factor object. Can be initialized in \code{alpha} and
+\code{epsilon} notation. Fractionation factors can be easily converted from values in one notation to values in
 another notation by using \code{\link{switch_notation}}.
 }
 \details{
+See \link{isotopia} for general information on initializing
+and converting to other isotope data objects.
 The \code{ff} function is a shorthand for \code{fractionation_factor} but otherwise identical.
 }
 \seealso{

man/get_value.Rd

@@ -3,15 +3,15 @@
 \alias{get_value}
 \title{Retrieve isotope object's primitive values}
 \usage{
-get_value(iso, notation = "raw")
+get_value(iso, notation = iso@notation)
 }
 \arguments{
 \item{notation}{specifiy which notation to return the value in (default is the notation
-that hte object is in)}
+that the object is in)}
 }
 \value{
 In the case of a single isotope object (Isoval), returns the numeric
-vector of raw values stored in the object (same as \code{\link{as.numeric}}).
+vector of raw values stored in the object (same as \code{\link[base]{as.numeric}}).
 In the case of an isotope system (Isosys),
 returns the data frame underlying the object with all its isotope value
 objects also replaced with their numeric raw values. To just get the data
@@ -22,7 +22,7 @@ This function returns an isotope object's (single value or isotope system)
 primitive data value(s).
 }
 \seealso{
-\code{\link{as.numeric}}, \code{\link{as.data.frame}}, \code{\link[base]{as.data.frame}} (base method)
+\code{\link[base]{as.numeric}}, \code{\link{as.data.frame}}, \code{\link[base]{as.data.frame}} (base method)
 
 Other data type attributes: \code{\link{get_label}},
   \code{\link{get_name}}, \code{\link{get_units}};

man/mass_balance.Rd

@@ -3,13 +3,13 @@
 \alias{mass_balance}
 \title{Calculate isotope mass balance}
 \usage{
-mass_balance(iso, iso2, ..., exact = exact_mass_balance())
+mass_balance(iso, iso2, ..., exact = get_iso_opts("exact_mass_balance"))
 }
 \arguments{
 \item{...}{- any number of weighted isotope value objects (have to be all either abundance or delta)}
 
-\item{exact}{- whether to calculate mass balance of delta values exactly (default FALSE),
-use exact_mass_balance to set this paramter globally}
+\item{exact}{- whether to calculate mass balance of delta values exactly (default FALSE), not
+fully implemented yet}
 }
 \value{
 weighted abundance or delta value object that represents the combination of the parameters

man/quietly.Rd

@@ -8,7 +8,7 @@ quietly(expr)
 \description{
 This small utility function is just a convenient wrapper for running
 isotope calculations silently without outputting any of the warnings or
-messages (it uses \link{suppressMessages} and \link{suppressWarnings}
+messages (it uses \link[base]{suppressMessages} and \link[base]{suppressWarnings}
 internally) that might occur. Use with care to suppress warnings, you
 might end up hiding important information.
 }

man/to_ff.Rd

@@ -17,7 +17,7 @@ isotope \code{\link{fraction_factor}} object if parameters can be converted, an
 Calculate/convert to an isotope \code{\link{fractionation_factor}}
 }
 \details{
-The \code{frac_factor(...)} function calculates the fractionation factor between two isotope data objects
+The \code{to_ff(...)} function calculates the fractionation factor between two isotope data objects
 (for example two \code{\link{delta}} values, two \code{\link{ratio}}, or two \code{\link{ff}}).
 All calculatinos are only permissible if the isotope values have matching
 attributes and fractionation factors will be returend in the default notation

tests/testthat/test-05-data.R

@@ -14,7 +14,7 @@ test_that("Testing that reference standards can be properly registered and retri
     expect_error(get_standard(name = "VSMOW"), "More than one")
     expect_error(get_standard(minor = "3H"), "No reference ratio registered")
     expect_equal(get_standard(minor = "2H", major = "1H", name = "VSMOW"), ratio(`2H` = 0.00015575, major = "1H", compound = "VSMOW"))
-    expect_message(to_ratio(delta(`2H` = -100, major = "1H", ref = "VSMOW")), "Successfully found a matching standard")
+    expect_message(to_ratio(delta(`2H` = -100, major = "1H", ref = "VSMOW")), "Successfully found a registered standard")
     expect_equal(to_ratio(delta(`2H` = 100, major = "1H", ref = "VSMOW")), ratio(`2H` = 1.1 * 0.00015575, major = "1H"))
     expect_is(get_iso_opts("standards"), "data.frame")
 })