Use roxygen for functions and methods

1 files changed, 35 insertions, 9 deletions

diff --git a/R/SFORB.solution.R b/R/SFORB.solution.R
index 4cb94def..2abe4577 100644
--- a/R/SFORB.solution.R
+++ b/R/SFORB.solution.R
@@ -1,9 +1,35 @@
-SFORB.solution = function(t, parent.0, k_12, k_21, k_1output) {

-  sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21)

-  b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp

-  b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp

-

-  parent = parent.0 *

-        (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +

-        ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))

-}

+#' Single First-Order Reversible Binding kinetics
+#' 
+#' Function describing the solution of the differential equations describing
+#' the kinetic model with first-order terms for a two-way transfer from a free
+#' to a bound fraction, and a first-order degradation term for the free
+#' fraction.  The initial condition is a defined amount in the free fraction
+#' and no substance in the bound fraction.
+#' 
+#' @param t Time.
+#' @param parent.0 Starting value for the response variable at time zero.
+#' @param k_12 Kinetic constant describing transfer from free to bound.
+#' @param k_21 Kinetic constant describing transfer from bound to free.
+#' @param k_1output Kinetic constant describing degradation of the free
+#'   fraction.
+#' @return The value of the response variable, which is the sum of free and
+#'   bound fractions at time \code{t}.
+#' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
+#'   and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+#'   EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+#'   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+#'   \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+#' @examples
+#' 
+#'   \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)}
+#' 
+#' @export
+SFORB.solution = function(t, parent.0, k_12, k_21, k_1output) {
+  sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21)
+  b1 = 0.5 * (k_12 + k_21 + k_1output) + sqrt_exp
+  b2 = 0.5 * (k_12 + k_21 + k_1output) - sqrt_exp
+
+  parent = parent.0 *
+        (((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +
+        ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t))
+}