From 56415f3c0638725aaa77db2c02eeaf9d4983452b Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Tue, 8 Nov 2022 08:46:57 +0100
Subject: Show DFOP g equivalent of SFORB in summary, test

---
 R/endpoints.R       |  6 ++++--
 R/summary.mkinfit.R | 13 +++++++------
 2 files changed, 11 insertions(+), 8 deletions(-)

(limited to 'R')

diff --git a/R/endpoints.R b/R/endpoints.R
index 227671b5..4aec8aa8 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -162,6 +162,7 @@ endpoints <- function(fit) {
       sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 - 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
+      g = (k_12 + k_21 - b1)/(b2 - b1)
 
       DT50_b1 = log(2)/b1
       DT50_b2 = log(2)/b2
@@ -169,8 +170,7 @@ endpoints <- function(fit) {
       DT90_b2 = log(10)/b2
 
       SFORB_fraction = function(t) {
-        ((k_12 + k_21 - b1)/(b2 - b1)) * exp(-b1 * t) +
-        ((k_12 + k_21 - b2)/(b1 - b2)) * exp(-b2 * t)
+        g * exp(-b1 * t) + (1 - g) * exp(-b2 * t)
       }
 
       f_50 <- function(log_t) (SFORB_fraction(exp(log_t)) - 0.5)^2
@@ -195,6 +195,8 @@ endpoints <- function(fit) {
       # Return the eigenvalues for comparison with DFOP rate constants
       ep$SFORB[[paste(obs_var, "b1", sep="_")]] = b1
       ep$SFORB[[paste(obs_var, "b2", sep="_")]] = b2
+      # Return g for comparison with DFOP
+      ep$SFORB[[paste(obs_var, "g", sep="_")]] = g
 
       ep$distimes[obs_var, c("DT50back")] = DT50_back
       ep$distimes[obs_var, c(paste("DT50", obs_var, "b1", sep = "_"))] = DT50_b1
diff --git a/R/summary.mkinfit.R b/R/summary.mkinfit.R
index 4122873f..c25b836e 100644
--- a/R/summary.mkinfit.R
+++ b/R/summary.mkinfit.R
@@ -6,14 +6,14 @@
 #' and optionally the data, consisting of observed, predicted and residual
 #' values.
 #'
-#' @param object an object of class \code{\link{mkinfit}}.
+#' @param object an object of class [mkinfit].
 #' @param x an object of class \code{summary.mkinfit}.
 #' @param data logical, indicating whether the data should be included in the
-#'   summary.
+#' summary.
 #' @param distimes logical, indicating whether DT50 and DT90 values should be
-#'   included.
+#' included.
 #' @param alpha error level for confidence interval estimation from t
-#'   distribution
+#' distribution
 #' @param digits Number of digits to use for printing
 #' @param \dots optional arguments passed to methods like \code{print}.
 #' @importFrom stats qt pt cov2cor
@@ -37,7 +37,8 @@
 #'   \item{ff}{The estimated formation fractions derived from the fitted
 #'      model.}
 #'   \item{distimes}{The DT50 and DT90 values for each observed variable.}
-#'   \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.}
+#'   \item{SFORB}{If applicable, eigenvalues and fractional eigenvector component
+#'      g of SFORB systems in the model.}
 #'   The print method is called for its side effect, i.e. printing the summary.
 #' @author Johannes Ranke
 #' @references FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence
@@ -264,7 +265,7 @@ print.summary.mkinfit <- function(x, digits = max(3, getOption("digits") - 3), .
 
   printSFORB <- !is.null(x$SFORB)
   if(printSFORB){
-    cat("\nEstimated Eigenvalues of SFORB model(s):\n")
+    cat("\nEstimated Eigenvalues and DFOP g parameter of SFORB model(s):\n")
     print(x$SFORB, digits=digits,...)
   }
 
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