Simplify SFORB also in the endpoint function

3 files changed, 31 insertions, 33 deletions

diff --git a/R/endpoints.R b/R/endpoints.R
index e81e7a0a..227671b5 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -10,18 +10,17 @@
 #' Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from
 #' HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models
 #'
-#' @param fit An object of class [mkinfit], [nlme.mmkin] or [saem.mmkin],
-#'  or another object that has list components
-#'  mkinmod containing an [mkinmod] degradation model, and two numeric vectors,
-#'  bparms.optim and bparms.fixed, that contain parameter values
-#'  for that model.
+#' @param fit An object of class [mkinfit], [nlme.mmkin] or [saem.mmkin], or
+#' another object that has list components mkinmod containing an [mkinmod]
+#' degradation model, and two numeric vectors, bparms.optim and bparms.fixed,
+#' that contain parameter values for that model.
 #' @importFrom stats optimize
-#' @return A list with a matrix of dissipation times named distimes,
-#'   and, if applicable, a vector of formation fractions named ff
-#'   and, if the SFORB model was in use, a vector of eigenvalues
-#'   of these SFORB models, equivalent to DFOP rate constants
+#' @return A list with a matrix of dissipation times named distimes, and, if
+#' applicable, a vector of formation fractions named ff and, if the SFORB model
+#' was in use, a vector of eigenvalues of these SFORB models, equivalent to
+#' DFOP rate constants
 #' @note The function is used internally by [summary.mkinfit],
-#'   [summary.nlme.mmkin] and [summary.saem.mmkin].
+#' [summary.nlme.mmkin] and [summary.saem.mmkin].
 #' @author Johannes Ranke
 #' @examples
 #'
@@ -160,7 +159,7 @@ endpoints <- function(fit) {
       k_12 = degparms[paste("k", obs_var, "free", "bound", sep="_")]
       k_21 = degparms[paste("k", obs_var, "bound", "free", sep="_")]
 
-      sqrt_exp = sqrt(1/4 * (k_12 + k_21 + k_1output)^2 + k_12 * k_21 - (k_12 + k_1output) * k_21)
+      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
 
diff --git a/log/test.log b/log/test.log
index 52b92245..b82e290f 100644
--- a/log/test.log
+++ b/log/test.log
@@ -1,53 +1,53 @@
 ℹ Testing mkin
 ✔ | F W S  OK | Context
 ✔ |         5 | AIC calculation
-✔ |         5 | Analytical solutions for coupled models [3.3s]
+✔ |         5 | Analytical solutions for coupled models [3.2s]
 ✔ |         5 | Calculation of Akaike weights
 ✔ |         3 | Export dataset for reading into CAKE
 ✔ |        12 | Confidence intervals and p-values [1.0s]
-✔ |     1  12 | Dimethenamid data from 2018 [31.5s]
+✔ |     1  12 | Dimethenamid data from 2018 [32.4s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_dmta.R:98:3): Different backends get consistent results for SFO-SFO3+, dimethenamid data
 Reason: Fitting this ODE model with saemix takes about 15 minutes on my system
 ────────────────────────────────────────────────────────────────────────────────
-✔ |        14 | Error model fitting [4.9s]
+✔ |        14 | Error model fitting [5.0s]
 ✔ |         5 | Time step normalisation
 ✔ |         4 | Calculation of FOCUS chi2 error levels [0.6s]
 ✔ |        14 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [0.8s]
-✔ |         4 | Test fitting the decline of metabolites from their maximum [0.4s]
+✔ |         4 | Test fitting the decline of metabolites from their maximum [0.3s]
 ✔ |         1 | Fitting the logistic model [0.2s]
-✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [23.7s]
+✔ |        10 | Batch fitting and diagnosing hierarchical kinetic models [24.5s]
 ✔ |     1  12 | Nonlinear mixed-effects models [0.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_mixed.R:74:3): saemix results are reproducible for biphasic fits
 Reason: Fitting with saemix takes around 10 minutes when using deSolve
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         3 | Test dataset classes mkinds and mkindsg
-✔ |        10 | Special cases of mkinfit calls [0.5s]
+✔ |        10 | Special cases of mkinfit calls [0.6s]
 ✔ |         3 | mkinfit features [0.7s]
 ✔ |         8 | mkinmod model generation and printing [0.2s]
 ✔ |         3 | Model predictions with mkinpredict [0.3s]
 ✔ |         7 | Multistart method for saem.mmkin models [36.3s]
-✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.3s]
-✔ |         9 | Nonlinear mixed-effects models with nlme [8.9s]
-✔ |        16 | Plotting [10.0s]
+✔ |        16 | Evaluations according to 2015 NAFTA guidance [2.5s]
+✔ |         9 | Nonlinear mixed-effects models with nlme [9.1s]
+✔ |        16 | Plotting [10.3s]
 ✔ |         4 | Residuals extracted from mkinfit models
-✔ |     1  37 | saemix parent models [72.0s]
+✔ |     1  37 | saemix parent models [72.3s]
 ────────────────────────────────────────────────────────────────────────────────
 Skip (test_saemix_parent.R:153:3): We can also use mkin solution methods for saem
 Reason: This still takes almost 2.5 minutes although we do not solve ODEs
 ────────────────────────────────────────────────────────────────────────────────
 ✔ |         2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4s]
 ✔ |        11 | Processing of residue series
-✔ |         7 | Fitting the SFORB model [3.7s]
+✔ |         7 | Fitting the SFORB model [3.8s]
 ✔ |         1 | Summaries of old mkinfit objects
 ✔ |         5 | Summary [0.2s]
 ✔ |         4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.2s]
 ✔ |         9 | Hypothesis tests [8.1s]
-✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4s]
+✔ |         4 | Calculation of maximum time weighted average concentrations (TWAs) [2.2s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 216.5 s
+Duration: 219.0 s
 
 ── Skipped tests  ──────────────────────────────────────────────────────────────
 • Fitting this ODE model with saemix takes about 15 minutes on my system (1)
diff --git a/man/endpoints.Rd b/man/endpoints.Rd
index 75fa9503..e3663aec 100644
--- a/man/endpoints.Rd
+++ b/man/endpoints.Rd
@@ -8,17 +8,16 @@ with mkinfit}
 endpoints(fit)
 }
 \arguments{
-\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or \link{saem.mmkin},
-or another object that has list components
-mkinmod containing an \link{mkinmod} degradation model, and two numeric vectors,
-bparms.optim and bparms.fixed, that contain parameter values
-for that model.}
+\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or \link{saem.mmkin}, or
+another object that has list components mkinmod containing an \link{mkinmod}
+degradation model, and two numeric vectors, bparms.optim and bparms.fixed,
+that contain parameter values for that model.}
 }
 \value{
-A list with a matrix of dissipation times named distimes,
-and, if applicable, a vector of formation fractions named ff
-and, if the SFORB model was in use, a vector of eigenvalues
-of these SFORB models, equivalent to DFOP rate constants
+A list with a matrix of dissipation times named distimes, and, if
+applicable, a vector of formation fractions named ff and, if the SFORB model
+was in use, a vector of eigenvalues of these SFORB models, equivalent to
+DFOP rate constants
 }
 \description{
 This function calculates DT50 and DT90 values as well as formation fractions