Cleaning up documentation

ApfeldLab · Jun 6, 2020 · 1856ba6 · 1856ba6
1 parent dc4632e
commit 1856ba6
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Showing 60 changed files with 3,359 additions and 489 deletions.
diff --git a/NAMESPACE b/NAMESPACE
@@ -1,6 +1,5 @@
 # Generated by roxygen2: do not edit by hand
 
-export("getAbsError-R")
 export(E)
 export(Error_E)
 export(Error_general)
@@ -16,34 +15,22 @@ export(create_error_df_pLigand)
 export(create_error_df_redox)
 export(create_error_df_redox_multiple)
 export(create_ranges_multiple)
-export(error_df)
 export(formatSpectraData)
 export(fraction_deprot)
-export(getAbsError)
 export(getDb)
-export(getE)
-export(getE_deriv)
-export(getErrorTable)
-export(getFractionMax)
-export(getProperty)
-export(getR)
-export(getpH)
 export(launchApp)
 export(newSensorFromSpectra)
 export(pH)
 export(pLigand)
-export(plotFractionMax)
-export(plotProperty)
-export(plotSpectra)
 export(plot_ranges_redox)
-export(rangePlot)
 export(ranges_df)
 export(rescaleToRange)
 export(spectraMatrixFromValues)
 exportClasses(Sensor)
 exportClasses(pHSensor)
 exportClasses(redoxSensor)
 exportClasses(sensorSpectra)
+exportMethods("getAbsError-R")
 exportMethods(error_df)
 exportMethods(getAbsError)
 exportMethods(getE)

diff --git a/R/Sensor_Methods.R b/R/Sensor_Methods.R
@@ -9,7 +9,7 @@
 #' @return A numeric array
 #'
 #' @family getR-methods
-#' @export
+#' @noRd
 setGeneric(
   "getR",
   def = function(object, ...) {
@@ -75,7 +75,7 @@ setMethod(
 #'
 #' @return A generic function for getFractionMax
 #'
-#' @export
+#' @noRd
 setGeneric(
   "getFractionMax",
   def = function(object, ...) {
@@ -96,7 +96,6 @@ setGeneric(
 #'
 #' @export
 #' @docType methods
-#' @rdname getFractionMax-methods
 #'
 #' @examples
 #' my_sensor <- new("Sensor", Rmin = 1, Rmax = 5, delta = 0.5)
@@ -119,8 +118,7 @@ setMethod(
 #'
 #' @return A function that gets the biochemical property of this sensor
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "getProperty",
   def = function(object, ...) {
@@ -137,8 +135,6 @@ setGeneric(
 #' in the maximum-emission state corresponding to the given R
 #'
 #' @export
-#' @docType methods
-#' @rdname getProperty-methods
 #'
 #' @examples
 #' my_sensor <- new("Sensor", Rmin = 1, Rmax = 5, delta = 0.5)
@@ -166,7 +162,6 @@ setMethod(
 #'
 #' @export
 #' @docType methods
-#' @rdname getProperty-redoxSensor
 setMethod(
   "getProperty",
   "redoxSensor",
@@ -186,8 +181,6 @@ setMethod(
 #' @return A numeric array of pH values
 #'
 #' @export
-#' @docType methods
-#' @rdname getProperty-pHSensor
 setMethod(
   "getProperty",
   "pHSensor",
@@ -204,8 +197,7 @@ setMethod(
 #'
 #' @return A numeric array of E values
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "getE",
   def = function(object, ...) {
@@ -227,8 +219,6 @@ setGeneric(
 #' @return A numeric array of E values
 #'
 #' @export
-#' @docType methods
-#' @rdname getE-redoxSensor
 setMethod(
   "getE",
   "redoxSensor",
@@ -252,8 +242,7 @@ setMethod(
 #'
 #' @return A numeric array of pH values
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "getpH",
   def = function(object, ...) {
@@ -273,8 +262,6 @@ setGeneric(
 #' @return A numeric array of pH values
 #'
 #' @export
-#' @docType methods
-#' @rdname getpH-pHSensor
 setMethod(
   "getpH",
   "pHSensor",
@@ -294,8 +281,7 @@ setMethod(
 #'
 #' @return A numeric array of dE/dR values
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "getE_deriv",
   def = function(object, ...) {
@@ -315,8 +301,6 @@ setGeneric(
 #' @return A numeric array of dE/dR values
 #'
 #' @export
-#' @docType methods
-#' @rdname getE_deriv-redoxSensor
 setMethod(
   "getE_deriv",
   "redoxSensor",
@@ -334,7 +318,7 @@ setMethod(
 #'
 #' @return A numeric error
 #'
-#' @export
+#' @noRd
 setGeneric(
   "getAbsError-R",
   def = function(object, ...) {
@@ -352,9 +336,8 @@ setGeneric(
 #' @param R A single numeric ratio value
 #' @param Error_Model A function in the form Error_Model(R) to Error in R
 #' @param ... Extra parameters applied to the FUN function
-#' @rdname getAbsError-R-redoxSensor
 #' @return A numeric error
-#'
+#' @export
 setMethod(
   "getAbsError-R",
   "redoxSensor",
@@ -376,8 +359,7 @@ setMethod(
 #'
 #' @return A numeric array of errors
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "getAbsError",
   def = function(object, ...) {
@@ -400,8 +382,6 @@ setGeneric(
 #' @return A numeric array of errors
 #'
 #' @export
-#' @docType methods
-#' @rdname getAbsError-sensor
 setMethod(
   "getAbsError",
   "Sensor",
@@ -450,8 +430,7 @@ setMethod(
 #'
 #' @return A dataframe of errors
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "getErrorTable",
   def = function(object, ...) {
@@ -477,8 +456,6 @@ setGeneric(
 #' @return A dataframe of errors
 #'
 #' @export
-#' @docType methods
-#' @rdname getErrorTable-sensor
 setMethod(
   "getErrorTable",
   "Sensor",
@@ -544,8 +521,7 @@ setMethod(
 #'
 #' @return A ggplot object
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "plotFractionMax",
   def = function(object, ...) {
@@ -565,8 +541,6 @@ setGeneric(
 #' @return A ggplot object
 #'
 #' @export
-#' @docType methods
-#' @rdname plotFractionMax-Sensor
 setMethod(
   "plotFractionMax",
   "Sensor",
@@ -596,8 +570,6 @@ setMethod(
 #' @return A ggplot object
 #'
 #' @export
-#' @docType methods
-#' @rdname plotFractionMax-redoxSensor
 setMethod(
   "plotFractionMax",
   "redoxSensor",
@@ -625,8 +597,6 @@ setMethod(
 #' @return A ggplot object
 #'
 #' @export
-#' @docType methods
-#' @rdname plotFractionMax-pHSensor
 setMethod(
   "plotFractionMax",
   "pHSensor",
@@ -653,8 +623,7 @@ setMethod(
 #'
 #' @return A ggplot object
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "plotProperty",
   def = function(object, ...) {
@@ -670,8 +639,6 @@ setGeneric(
 #' @return A ggplot object
 #'
 #' @export
-#' @docType methods
-#' @rdname plotProperty-Sensor
 setMethod(
   "plotProperty",
   "Sensor",
@@ -692,8 +659,6 @@ setMethod(
 #' @return A ggplot object
 #'
 #' @export
-#' @docType methods
-#' @rdname plotProperty-redoxSensor
 setMethod(
   "plotProperty",
   "redoxSensor",
@@ -721,8 +686,6 @@ setMethod(
 #' @return A ggplot object
 #'
 #' @export
-#' @docType methods
-#' @rdname plotProperty-pHSensor
 setMethod(
   "plotProperty",
   "pHSensor",
@@ -746,8 +709,7 @@ setMethod(
 #'
 #' @return An error dataframe
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
   "error_df",
   def = function(object, ...) {
@@ -784,7 +746,6 @@ setGeneric(
 #'   inaccuracies = c(0.01, 0.02), Emin = -300, Emax = -200,
 #' )
 #' @export
-#' @docType methods
 setMethod(
   "error_df",
   "redoxSensor",
@@ -812,7 +773,6 @@ setMethod(
 #' @return A ranges dataframe
 #'
 #' @export
-#' @docType methods
 setGeneric(
   "ranges_df",
   def = function(object, ...) {
@@ -847,7 +807,6 @@ setGeneric(
 #' my_sensor <- new("redoxSensor", new("Sensor", Rmin = 1, Rmax = 5, delta = 0.2), e0 = -250)
 #' ranges_df(my_sensor)
 #' @export
-#' @docType methods
 setMethod(
   "ranges_df",
   "redoxSensor",
@@ -872,8 +831,7 @@ setMethod(
 #'
 #' @return A ggplot object
 #'
-#' @export
-#' @docType methods
+#' @noRd
 setGeneric(
     "rangePlot",
     def = function(object, ...) {
@@ -898,7 +856,6 @@ setGeneric(
 #' my_sensor <- new("redoxSensor", new("Sensor", Rmin = 1, Rmax = 5, delta = 0.2), e0 = -250)
 #' rangePlot(my_sensor)
 #' @export
-#' @docType methods
 setMethod(
     "rangePlot",
     "redoxSensor",

diff --git a/R/Spectra_Methods.R b/R/Spectra_Methods.R
@@ -6,9 +6,7 @@
 
 #' @return A ggplot object
 #'
-#' @export
-#' @docType methods
-#' @rdname plotSpectra-generic
+#' @noRd
 #'
 #' @import ggplot2
 setGeneric('plotSpectra', def = function(object, ...) standardGeneric("plotSpectra"))
@@ -25,8 +23,6 @@ setGeneric('plotSpectra', def = function(object, ...) standardGeneric("plotSpect
 #' @return A ggplot object
 #'
 #' @export
-#' @docType methods
-#' @rdname plotSpectra-sensorSpectra
 setMethod('plotSpectra', "sensorSpectra", definition =
               function(object, minimum_name = "Minimum State", maximum_name = "Maximum State") {
                 spectraData <- data.frame(lambda = object@lambdas, min = object@values_minimum, max = object@values_maximum)