Reflow documentation

R/sensmodel.R

@@ -1,31 +1,36 @@
 #' Modeling spectral sensitivity
 #'
-#' Models spectral sensitivity (with oil droplets; optional) based on peak cone sensitivity
-#' according to the models of Govardovskii et al. (2000) and Hart & Vorobyev (2005).
+#' Models spectral sensitivity (with oil droplets; optional) based on peak cone
+#' sensitivity according to the models of Govardovskii et al. (2000) and Hart &
+#' Vorobyev (2005).
 #'
 #' @param peaksens (required) a vector with peak sensitivities for the cones to
-#' model.
-#' @param range a vector of length 2 for the range over which to calculate the spectral
-#' sensitivities (defaults to 300nm to 700nm).
-#' @param lambdacut a vector of same length as peaksens that lists the cut-off wavelength
-#' value for oil droplets. Needs either `Bmid` or `oiltype` to also be entered.
-#' See Hart and Vorobyev (2005).
-#' @param Bmid a vector of same length as peaksens that lists the gradient of line
-#' tangent to the absorbance spectrum of the oil droplets. See Hart and Vorobyev (2005).
-#' @param oiltype a list of same length as peaksens that lists the oil droplet types
-#' (currently accepts only "T", C", "Y", "R", "P") when Bmid is not known. Calculates
-#' Bmid based on the regression equations found in Hart ad Vorobyev (2005).
+#'   model.
+#' @param range a vector of length 2 for the range over which to calculate the
+#'   spectral sensitivities (defaults to 300nm to 700nm).
+#' @param lambdacut a vector of same length as peaksens that lists the cut-off
+#'   wavelength value for oil droplets. Needs either `Bmid` or `oiltype` to also
+#'   be entered. See Hart and Vorobyev (2005).
+#' @param Bmid a vector of same length as peaksens that lists the gradient of
+#'   line tangent to the absorbance spectrum of the oil droplets. See Hart and
+#'   Vorobyev (2005).
+#' @param oiltype a list of same length as peaksens that lists the oil droplet
+#'   types (currently accepts only "T", C", "Y", "R", "P") when Bmid is not
+#'   known. Calculates Bmid based on the regression equations found in Hart ad
+#'   Vorobyev (2005).
 #' @param beta logical. If `TRUE` the sensitivities will include the beta peak
 #' See Govardovskii et al.(2000) (defaults to `TRUE`).
-#' @param om a vector of same length as `range1`-`range2` that contains ocular media transmission data.
-#' If included, cone sensitivity will be corrected for ocular media transmission. Currently accepts "bird" using
-#' values from Hart et al. (2005), or user-defined values.
-#' @param integrate logical. If `TRUE`, each curve is transformed to have a total area
-#' under the curve of 1 (best for visual models; defaults to `TRUE`). NOTE:
-#' integration is applied before any effects of ocular media are considered, for
-#' compatibility with visual model procedures.
-#' @param sensnames A vector equal in length to `peaksens`, specifying custom names for the resulting sensitivity
-#' curves (e.g. c('s', 'm', 'l') for short-, medium- and long-wavelength sensitive receptors.)
+#' @param om a vector of same length as `range1`-`range2` that contains ocular
+#'   media transmission data. If included, cone sensitivity will be corrected
+#'   for ocular media transmission. Currently accepts "bird" using values from
+#'   Hart et al. (2005), or user-defined values.
+#' @param integrate logical. If `TRUE`, each curve is transformed to have a
+#'   total area under the curve of 1 (best for visual models; defaults to
+#'   `TRUE`). NOTE: integration is applied before any effects of ocular media
+#'   are considered, for compatibility with visual model procedures.
+#' @param sensnames A vector equal in length to `peaksens`, specifying custom
+#'   names for the resulting sensitivity curves (e.g. c('s', 'm', 'l') for
+#'   short-, medium- and long-wavelength sensitive receptors.)
 #'
 #' @return A data frame of class `rspec` containing each cone model as a column.
 #'
@@ -41,7 +46,9 @@
 #'
 #' # Danio aequipinnatus based on Govardovskii et al. (2000)
 #' daniosens <- sensmodel(c(357, 411, 477, 569))
-#' @author Pierre-Paul Bitton \email{bittonp@@uwindsor.ca}, Chad Eliason \email{cme16@@zips.uakron.edu}
+#'
+#' @author Pierre-Paul Bitton \email{bittonp@@uwindsor.ca}
+#' @author Chad Eliason \email{cme16@@zips.uakron.edu}
 #'
 #' @references Govardovskii VI, Fyhrquist N, Reuter T, Kuzmin DG and Donner K.
 #'   2000. In search of the visual pigment template. Visual Neuroscience