Another overhaul of analytical solutions

Still in preparation for analytical solutions of coupled models
author: Johannes Ranke <jranke@uni-bremen.de> 2020-05-07 22:13:33 +0200
committer: Johannes Ranke <jranke@uni-bremen.de> 2020-05-07 22:14:19 +0200
commit: 92bd33824bde6b6b21bfc7e30953092a74d3cce5 (patch)
tree: bb2e08ef15d8a4f4f7b04cf4f5312ec861ec1d1c
parent: 67c8163487e776e9a378c9dfcd39c74f6e6bc507 (diff)
45 files changed, 626 insertions, 390 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 96f4637d..5f38d12c 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: mkin
 Type: Package
 Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.49.11
-Date: 2020-05-20
+Version: 0.9.50
+Date: 2020-05-07
 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
                     email = "jranke@uni-bremen.de",
                     comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/NEWS.md b/NEWS.md
index ba1daa87..2512f361 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -2,6 +2,8 @@
 
 - Support SFORB with formation fractions
 
+- 'mkinmod': Make 'use_of_ff' = "max" the default
+
 # mkin 0.9.49.11 (2020-04-20)
 
 - Increase a test tolerance to make it pass on all CRAN check machines
diff --git a/R/create_deg_func.R b/R/create_deg_func.R
new file mode 100644
index 00000000..40efb3a3
--- /dev/null
+++ b/R/create_deg_func.R
@@ -0,0 +1,54 @@
+#' Create degradation functions for known analytical solutions
+#'
+#' @param spec List of model specifications as contained in mkinmod objects
+#' @param use_of_ff Minimum or maximum use of formation fractions
+#' @return Degradation function to be attached to mkinmod objects
+#' @examples
+#'
+#' SFO_SFO <- mkinmod(
+#'   parent = mkinsub("SFO", "m1"),
+#'   m1 = mkinsub("SFO"))
+#' fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+
+create_deg_func <- function(spec, use_of_ff = c("min", "max")) {
+
+  use_of_ff <- match.arg(use_of_ff)
+
+  min_ff <- use_of_ff == "min"
+
+  obs_vars <- names(spec)
+
+  n <- character(0)
+
+  parent <- obs_vars[1]
+
+  n[1] <- paste0(parent, " = ", spec[[1]]$type, ".solution(outtimes, odeini['", parent, 
+    if (spec[[1]]$type == "SFORB") "_free", "'], ",
+    switch(spec[[1]]$type,
+      SFO = paste0("k_", parent, if (min_ff) "_sink" else "", ")"),
+      FOMC = "alpha, beta)",
+      IORE = paste0("k__iore_", parent, if (min_ff) "_sink" else "", ", N_", parent, ")"),
+      DFOP = "k1, k2, g)",
+      SFORB = paste0("k_", parent, "_free_bound, k_", parent, "_bound_free, k_", parent, "_free", if (min_ff) "_sink" else "", ")"),
+      HS = "k1, k2, tb)",
+      logistic = "kmax, k0, r)"
+    )
+  )
+
+  all_n <- paste(n, collapse = ",\n")
+
+  f_body <- paste0("{\n",
+    "out <- with(as.list(odeparms), {\n",
+    "data.frame(\n",
+      "time = outtimes,\n",
+      all_n, "\n",
+    ")})\n",
+    "return(out)\n}\n"
+  )
+
+  deg_func <- function(odeini, odeparms, outtimes) {}
+
+  body(deg_func) <- parse(text = f_body)
+
+  return(deg_func)
+}
diff --git a/R/logistic.solution.R b/R/logistic.solution.R
deleted file mode 100644
index d9db13d7..00000000
--- a/R/logistic.solution.R
+++ /dev/null
@@ -1,59 +0,0 @@
-#' Logistic kinetics
-#' 
-#' Function describing exponential decline from a defined starting value, with
-#' an increasing rate constant, supposedly caused by microbial growth
-#' 
-#' @param t Time.
-#' @param parent.0 Starting value for the response variable at time zero.
-#' @param kmax Maximum rate constant.
-#' @param k0 Minumum rate constant effective at time zero.
-#' @param r Growth rate of the increase in the rate constant.
-#' @return The value of the response variable at time \code{t}.
-#' @note The solution of the logistic model reduces to the
-#'   \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.
-#' @references FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
-#'   and Degradation Kinetics from Environmental Fate Studies on Pesticides in
-#'   EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
-#'   Version 1.1, 18 December 2014
-#'   \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
-#' @examples
-#' 
-#'   # Reproduce the plot on page 57 of FOCUS (2014)
-#'   plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
-#'        from = 0, to = 100, ylim = c(0, 100),
-#'        xlab = "Time", ylab = "Residue")
-#'   plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
-#'        from = 0, to = 100, add = TRUE, lty = 2, col = 2)
-#'   plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
-#'        from = 0, to = 100, add = TRUE, lty = 3, col = 3)
-#'   plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
-#'        from = 0, to = 100, add = TRUE, lty = 4, col = 4)
-#'   plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
-#'        from = 0, to = 100, add = TRUE, lty = 5, col = 5)
-#'   legend("topright", inset = 0.05,
-#'          legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),
-#'                          ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),
-#'          lty = 1:5, col = 1:5)
-#' 
-#'   # Fit with synthetic data
-#'   logistic <- mkinmod(parent = mkinsub("logistic"))
-#' 
-#'   sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-#'   parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)
-#'   d_logistic <- mkinpredict(logistic,
-#'     parms_logistic, c(parent = 100),
-#'     sampling_times)
-#'   d_2_1 <- add_err(d_logistic,
-#'     sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
-#'     n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
-#' 
-#'   m <- mkinfit("logistic", d_2_1, quiet = TRUE)
-#'   plot_sep(m)
-#'   summary(m)$bpar
-#'   endpoints(m)$distimes
-#' 
-#' @export
-logistic.solution <- function(t, parent.0, kmax, k0, r)
-{
-	parent = parent.0 * (kmax / (kmax - k0 + k0 * exp (r * t))) ^(kmax/r)
-}
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 2b7e71cb..54dd75c2 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -269,7 +269,7 @@ mkinfit <- function(mkinmod, observed,
     if (mkinmod[[1]] %in% parent_models_available) {
       speclist <- list(list(type = mkinmod, sink = TRUE))
       names(speclist) <- presumed_parent_name
-      mkinmod <- mkinmod(speclist = speclist)
+      mkinmod <- mkinmod(speclist = speclist, use_of_ff = "min")
     } else {
       stop("Argument mkinmod must be of class mkinmod or a string containing one of\n  ",
            paste(parent_models_available, collapse = ", "))
diff --git a/R/mkinmod.R b/R/mkinmod.R
index f52baa4f..21551861 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -101,7 +101,7 @@
 #' }
 #'
 #' @export mkinmod
-mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verbose = FALSE)
+mkinmod <- function(..., use_of_ff = "max", speclist = NULL, quiet = FALSE, verbose = FALSE)
 {
   if (is.null(speclist)) spec <- list(...)
   else spec <- speclist
@@ -421,45 +421,8 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
   }
   # }}}
 
-  # Attach a degradation function if an analytical solution is available {{{
-  parent_type = spec[[1]]$type
-  parent_name = names(spec)[[1]]
-  if (length(spec) == 1) {
-    odeparm_map <- switch(parent_type,
-      SFO = c(
-        k = if(use_of_ff == "min") paste("k", parent_name, "sink", sep = "_")
-          else  paste("k", parent_name, sep = "_")),
-      FOMC = c(alpha = "alpha", beta = "beta"),
-      IORE = c(
-        k__iore = if(use_of_ff == "min") paste("k__iore", parent_name, "sink", sep = "_")
-          else paste("k__iore", parent_name, sep = "_"),
-        N = paste("N", parent_name, sep = "_")),
-      DFOP = c(k1 = "k1", k2 = "k2", g = "g"),
-      HS = c(k1 = "k1", k2 = "k2", tb = "tb"),
-      SFORB = c(
-        k_12 = paste("k", parent_name, "free_bound", sep = "_"),
-        k_21 = paste("k", parent_name, "bound_free", sep = "_"),
-        k_1output = paste("k", parent_name, "free_sink", sep = "_")),
-      logistic = c(kmax = "kmax", k0 = "k0", r = "r")
-    )
-    odeparm_rev_map <- names(odeparm_map)
-    names(odeparm_rev_map) <- odeparm_map
-
-    model$deg_func <- function(odeini, odeparms, outtimes) {
-      parent_func <- getFromNamespace(paste0(parent_type, ".solution"), "mkin")
-      odeparm_list <- as.list(odeparms)
-      names(odeparm_list) <- odeparm_rev_map[names(odeparm_list)]
-
-      values <- do.call(parent_func,
-        args = c(
-          list(t = outtimes, parent_0 = odeini[1]),
-          odeparm_list))
-      out <- data.frame(outtimes, values)
-      names(out) <- c("time", parent_name)
-      return(out)
-    }
-  }
-  # }}}
+  # Attach a degradation function if an analytical solution is available
+  model$deg_func <- create_deg_func(spec, use_of_ff)
 
   class(model) <- "mkinmod"
   return(model)
diff --git a/R/mkinpredict.R b/R/mkinpredict.R
index 0f8e83bb..df51dbe3 100644
--- a/R/mkinpredict.R
+++ b/R/mkinpredict.R
@@ -43,36 +43,36 @@
 #'
 #' SFO <- mkinmod(degradinol = mkinsub("SFO"))
 #' # Compare solution types
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       solution_type = "analytical")
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       solution_type = "deSolve")
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       solution_type = "deSolve", use_compiled = FALSE)
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       solution_type = "eigen")
 #'
 #' # Compare integration methods to analytical solution
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       solution_type = "analytical")[21,]
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       method = "lsoda")[21,]
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       method = "ode45")[21,]
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
 #'       method = "rk4")[21,]
 #' # rk4 is not as precise here
 #'
 #' # The number of output times used to make a lot of difference until the
 #' # default for atol was adjusted
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
 #'       seq(0, 20, by = 0.1))[201,]
-#' mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+#' mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
 #'       seq(0, 20, by = 0.01))[2001,]
 #'
 #' # Check compiled model versions - they are faster than the eigenvalue based solutions!
 #' SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
-#'                   m1 = list(type = "SFO"))
+#'                   m1 = list(type = "SFO"), use_of_ff = "min")
 #' if(require(rbenchmark)) {
 #'   benchmark(
 #'     eigen = mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
diff --git a/R/nlme.R b/R/nlme.R
index 60cd2ca1..fa69db3c 100644
--- a/R/nlme.R
+++ b/R/nlme.R
@@ -13,15 +13,15 @@
 #' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 #' m_SFO <- mkinmod(parent = mkinsub("SFO"))
 #' d_SFO_1 <- mkinpredict(m_SFO,
-#'   c(k_parent_sink = 0.1),
+#'   c(k_parent = 0.1),
 #'   c(parent = 98), sampling_times)
 #' d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
 #' d_SFO_2 <- mkinpredict(m_SFO,
-#'   c(k_parent_sink = 0.05),
+#'   c(k_parent = 0.05),
 #'   c(parent = 102), sampling_times)
 #' d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
 #' d_SFO_3 <- mkinpredict(m_SFO,
-#'   c(k_parent_sink = 0.02),
+#'   c(k_parent = 0.02),
 #'   c(parent = 103), sampling_times)
 #' d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
 #'
diff --git a/R/parent_solutions.R b/R/parent_solutions.R
index c33d6d13..e02bcda7 100644
--- a/R/parent_solutions.R
+++ b/R/parent_solutions.R
@@ -136,7 +136,7 @@ DFOP.solution <- function(t, parent_0, k1, k2, g)
 #' between them.
 #' 
 #' @family parent solutions
-#' @inherit HS.solution 
+#' @inherit DFOP.solution 
 #' @param tb Break point. Before this time, exponential decline according to
 #'   \code{k1} is calculated, after this time, exponential decline proceeds
 #'   according to \code{k2}.
@@ -161,7 +161,7 @@ HS.solution <- function(t, parent_0, k1, k2, tb)
 #' and no substance in the bound fraction.
 #' 
 #' @family parent solutions
-#' @inherit HS.solution 
+#' @inherit SFO.solution 
 #' @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
diff --git a/build.log b/build.log
index e1e92209..b3df3235 100644
--- a/build.log
+++ b/build.log
@@ -5,5 +5,5 @@
 * creating vignettes ... OK
 * checking for LF line-endings in source and make files and shell scripts
 * checking for empty or unneeded directories
-* building ‘mkin_0.9.49.11.tar.gz’
+* building ‘mkin_0.9.50.tar.gz’
 
diff --git a/check.log b/check.log
index ddf3c6f4..cc24b711 100644
--- a/check.log
+++ b/check.log
@@ -5,7 +5,7 @@
 * using options ‘--no-tests --as-cran’
 * checking for file ‘mkin/DESCRIPTION’ ... OK
 * checking extension type ... Package
-* this is package ‘mkin’ version ‘0.9.49.11’
+* this is package ‘mkin’ version ‘0.9.50’
 * package encoding: UTF-8
 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
 Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
diff --git a/docs/404.html b/docs/404.html
index 12d9b275..c6da911d 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 40f16c15..7091d4c9 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
diff --git a/docs/authors.html b/docs/authors.html
index 9bba91ac..bc170e49 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
diff --git a/docs/index.html b/docs/index.html
index 546f9143..5c4a0a9b 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
diff --git a/docs/news/index.html b/docs/news/index.html
index 07f733dd..bc69fd2d 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -143,7 +143,9 @@
 <a href="#mkin-0-9-50-1-unreleased" class="anchor"></a>mkin 0.9.50.1 (unreleased)<small> Unreleased </small>
 </h1>
 <ul>
-<li>Support SFORB with formation fractions</li>
+<li><p>Support SFORB with formation fractions</p></li>
+<li><p>‘mkinmod’: Make ‘use_of_ff’ = “max” the default</p></li>
+<li><p>Implement analytical solutions for some coupled models, e.g. SFO-SFO, DFOP-SFO, SFORB-SFO</p></li>
 </ul>
 </div>
     <div id="mkin-0-9-49-11-2020-04-20" class="section level1">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index 6489b012..32bcaa05 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
   NAFTA_examples: web_only/NAFTA_examples.html
   benchmarks: web_only/benchmarks.html
   compiled_models: web_only/compiled_models.html
-last_built: 2020-05-07T07:07Z
+last_built: 2020-05-07T20:11Z
 urls:
   reference: https://pkgdown.jrwb.de/mkin/reference
   article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html
index 46e0cc91..84e33f9e 100644
--- a/docs/reference/DFOP.solution.html
+++ b/docs/reference/DFOP.solution.html
@@ -73,7 +73,7 @@ two exponential decline functions." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html
index 6c1f5229..369398d5 100644
--- a/docs/reference/FOMC.solution.html
+++ b/docs/reference/FOMC.solution.html
@@ -73,7 +73,7 @@ a decreasing rate constant." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html
index ad33d948..2684ee60 100644
--- a/docs/reference/HS.solution.html
+++ b/docs/reference/HS.solution.html
@@ -73,7 +73,7 @@ between them." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -152,6 +152,22 @@ between them.</p>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
+      <th>t</th>
+      <td><p>Time.</p></td>
+    </tr>
+    <tr>
+      <th>parent_0</th>
+      <td><p>Starting value for the response variable at time zero.</p></td>
+    </tr>
+    <tr>
+      <th>k1</th>
+      <td><p>First kinetic constant.</p></td>
+    </tr>
+    <tr>
+      <th>k2</th>
+      <td><p>Second kinetic constant.</p></td>
+    </tr>
+    <tr>
       <th>tb</th>
       <td><p>Break point. Before this time, exponential decline according to
 <code>k1</code> is calculated, after this time, exponential decline proceeds
@@ -159,6 +175,21 @@ according to <code>k2</code>.</p></td>
     </tr>
     </table>
 
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>The value of the response variable at time <code>t</code>.</p>
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>Other parent solutions: 
diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html
index 93da04eb..9664deb3 100644
--- a/docs/reference/SFO.solution.html
+++ b/docs/reference/SFO.solution.html
@@ -72,7 +72,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html
index c9f1b471..504f209f 100644
--- a/docs/reference/SFORB.solution.html
+++ b/docs/reference/SFORB.solution.html
@@ -76,7 +76,7 @@ and no substance in the bound fraction." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -158,6 +158,14 @@ and no substance in the bound fraction.</p>
     <table class="ref-arguments">
     <colgroup><col class="name" /><col class="desc" /></colgroup>
     <tr>
+      <th>t</th>
+      <td><p>Time.</p></td>
+    </tr>
+    <tr>
+      <th>parent_0</th>
+      <td><p>Starting value for the response variable at time zero.</p></td>
+    </tr>
+    <tr>
       <th>k_12</th>
       <td><p>Kinetic constant describing transfer from free to bound.</p></td>
     </tr>
@@ -176,6 +184,18 @@ fraction.</p></td>
 
     <p>The value of the response variable, which is the sum of free and
   bound fractions at time <code>t</code>.</p>
+    <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
+
+    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a></p>
     <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2>
 
     <div class='dont-index'><p>Other parent solutions: 
diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html
new file mode 100644
index 00000000..e14857cc
--- /dev/null
+++ b/docs/reference/create_deg_func.html
@@ -0,0 +1,198 @@
+<!-- Generated by pkgdown: do not edit by hand -->
+<!DOCTYPE html>
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+      <a href="../articles/mkin.html">Introduction to mkin</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_D.html">Example evaluation of FOCUS Example Dataset D</a>
+    </li>
+    <li>
+      <a href="../articles/FOCUS_L.html">Example evaluation of FOCUS Laboratory Data L1 to L3</a>
+    </li>
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+      <a href="../articles/web_only/FOCUS_Z.html">Example evaluation of FOCUS Example Dataset Z</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/compiled_models.html">Performance benefit by using compiled model definitions in mkin</a>
+    </li>
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+      <a href="../articles/twa.html">Calculation of time weighted average concentrations with mkin</a>
+    </li>
+    <li>
+      <a href="../articles/web_only/NAFTA_examples.html">Example evaluation of NAFTA SOP Attachment examples</a>
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+      </header>
+
+<div class="row">
+  <div class="col-md-9 contents">
+    <div class="page-header">
+    <h1>Create degradation functions for known analytical solutions</h1>
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/create_deg_func.R'><code>R/create_deg_func.R</code></a></small>
+    <div class="hidden name"><code>create_deg_func.Rd</code></div>
+    </div>
+
+    <div class="ref-description">
+    <p>Create degradation functions for known analytical solutions</p>
+    </div>
+
+    <pre class="usage"><span class='fu'>create_deg_func</span>(<span class='no'>spec</span>, <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"min"</span>, <span class='st'>"max"</span>))</pre>
+
+    <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
+    <table class="ref-arguments">
+    <colgroup><col class="name" /><col class="desc" /></colgroup>
+    <tr>
+      <th>spec</th>
+      <td><p>List of model specifications as contained in mkinmod objects</p></td>
+    </tr>
+    <tr>
+      <th>use_of_ff</th>
+      <td><p>Minimum or maximum use of formation fractions</p></td>
+    </tr>
+    </table>
+
+    <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
+
+    <p>Degradation function to be attached to mkinmod objects</p>
+
+    <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2>
+    <pre class="examples"><div class='input'>
+<span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
+  <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
+  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='no'>fit</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_2006_D</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; <span class='warning'>Warning: Observations with value of zero were removed from the data</span></div></pre>
+  </div>
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
+  </div>
+</div>
+
+
+      <footer>
+      <div class="copyright">
+  <p>Developed by Johannes Ranke.</p>
+</div>
+
+<div class="pkgdown">
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
+</div>
+
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+   </div>
+
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diff --git a/docs/reference/index.html b/docs/reference/index.html
index f77881fe..75820166 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -609,7 +609,7 @@ kinetic models fitted with mkinfit</p></td>
       </tr><tr>
         
         <td>
-          <p><code><a href="logistic.solution.html">logistic.solution()</a></code> <code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
+          <p><code><a href="logistic.solution.html">logistic.solution()</a></code> </p>
         </td>
         <td><p>Logistic kinetics</p></td>
       </tr>
diff --git a/docs/reference/logistic.solution.html b/docs/reference/logistic.solution.html
index 9697d420..b0ec77b1 100644
--- a/docs/reference/logistic.solution.html
+++ b/docs/reference/logistic.solution.html
@@ -41,8 +41,6 @@
 
 <meta property="og:title" content="Logistic kinetics — logistic.solution" />
 <meta property="og:description" content="Function describing exponential decline from a defined starting value, with
-an increasing rate constant, supposedly caused by microbial growth
-Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth" />
 
 
@@ -75,7 +73,7 @@ an increasing rate constant, supposedly caused by microbial growth" />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -139,20 +137,16 @@ an increasing rate constant, supposedly caused by microbial growth" />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Logistic kinetics</h1>
-    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/logistic.solution.R'><code>R/logistic.solution.R</code></a>, <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/parent_solutions.R'><code>R/parent_solutions.R</code></a></small>
     <div class="hidden name"><code>logistic.solution.Rd</code></div>
     </div>
 
     <div class="ref-description">
     <p>Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth</p>
-<p>Function describing exponential decline from a defined starting value, with
-an increasing rate constant, supposedly caused by microbial growth</p>
     </div>
 
-    <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)
-
-<span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
+    <pre class="usage"><span class='fu'>logistic.solution</span>(<span class='no'>t</span>, <span class='no'>parent_0</span>, <span class='no'>kmax</span>, <span class='no'>k0</span>, <span class='no'>r</span>)</pre>
 
     <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2>
     <table class="ref-arguments">
@@ -177,10 +171,6 @@ an increasing rate constant, supposedly caused by microbial growth</p>
       <th>r</th>
       <td><p>Growth rate of the increase in the rate constant.</p></td>
     </tr>
-    <tr>
-      <th>parent.0</th>
-      <td><p>Starting value for the response variable at time zero.</p></td>
-    </tr>
     </table>
 
     <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2>
@@ -190,11 +180,14 @@ an increasing rate constant, supposedly caused by microbial growth</p>
 
     <p>The solution of the logistic model reduces to the
   <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
-<p>The solution of the logistic model reduces to the
-  <code><a href='SFO.solution.html'>SFO.solution</a></code> if <code>k0</code> is equal to <code>kmax</code>.</p>
     <h2 class="hasAnchor" id="references"><a class="anchor" href="#references"></a>References</h2>
 
-    <p>FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
+    <p>FOCUS (2006) &#8220;Guidance Document on Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
+  EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
+  <a href='http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics'>http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics</a>
+FOCUS (2014) &#8220;Generic guidance for Estimating Persistence
   and Degradation Kinetics from Environmental Fate Studies on Pesticides in
   EU Registration&#8221; Report of the FOCUS Work Group on Degradation Kinetics,
   Version 1.1, 18 December 2014
@@ -248,44 +241,6 @@ an increasing rate constant, supposedly caused by microbial growth</p>
 #&gt; r          1.1821120
 #&gt; sigma      7.3256566</div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt;            DT50     DT90  DT50_k0 DT50_kmax
 #&gt; parent 36.86533 62.41511 4297.853  10.83349</div><div class='input'>
-
-  <span class='co'># Reproduce the plot on page 57 of FOCUS (2014)</span>
-  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.2</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>ylim</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>100</span>),
-       <span class='kw'>xlab</span> <span class='kw'>=</span> <span class='st'>"Time"</span>, <span class='kw'>ylab</span> <span class='kw'>=</span> <span class='st'>"Residue"</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.4</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.8</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>3</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>3</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.001</span>, <span class='fl'>0.2</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>4</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>4</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'>logistic.solution</span>(<span class='no'>x</span>, <span class='fl'>100</span>, <span class='fl'>0.08</span>, <span class='fl'>0.08</span>, <span class='fl'>0.2</span>),
-       <span class='kw'>from</span> <span class='kw'>=</span> <span class='fl'>0</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>add</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>, <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>5</span>)</div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></span>(<span class='st'>"topright"</span>, <span class='kw'>inset</span> <span class='kw'>=</span> <span class='fl'>0.05</span>,
-         <span class='kw'>legend</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span>(<span class='st'>"k0 = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.0001</span>, <span class='fl'>0.001</span>, <span class='fl'>0.08</span>),
-                         <span class='st'>", r = "</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0.2</span>, <span class='fl'>0.4</span>, <span class='fl'>0.8</span>, <span class='fl'>0.2</span>, <span class='fl'>0.2</span>)),
-         <span class='kw'>lty</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>, <span class='kw'>col</span> <span class='kw'>=</span> <span class='fl'>1</span>:<span class='fl'>5</span>)</div><div class='img'><img src='logistic.solution-3.png' alt='' width='700' height='433' /></div><div class='input'>
-  <span class='co'># Fit with synthetic data</span>
-  <span class='no'>logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"logistic"</span>))
-
-  <span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
-  <span class='no'>parms_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>kmax</span> <span class='kw'>=</span> <span class='fl'>0.08</span>, <span class='kw'>k0</span> <span class='kw'>=</span> <span class='fl'>0.0001</span>, <span class='kw'>r</span> <span class='kw'>=</span> <span class='fl'>0.2</span>)
-  <span class='no'>d_logistic</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>logistic</span>,
-    <span class='no'>parms_logistic</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>),
-    <span class='no'>sampling_times</span>)
-  <span class='no'>d_2_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_logistic</span>,
-    <span class='kw'>sdfunc</span> <span class='kw'>=</span> <span class='kw'>function</span>(<span class='no'>x</span>) <span class='fu'><a href='sigma_twocomp.html'>sigma_twocomp</a></span>(<span class='no'>x</span>, <span class='fl'>0.5</span>, <span class='fl'>0.07</span>),
-    <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>reps</span> <span class='kw'>=</span> <span class='fl'>2</span>, <span class='kw'>digits</span> <span class='kw'>=</span> <span class='fl'>5</span>, <span class='kw'>LOD</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>seed</span> <span class='kw'>=</span> <span class='fl'>123456</span>)<span class='kw'>[[</span><span class='fl'>1</span>]]
-
-  <span class='no'>m</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='st'>"logistic"</span>, <span class='no'>d_2_1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)
-  <span class='fu'><a href='plot.mkinfit.html'>plot_sep</a></span>(<span class='no'>m</span>)</div><div class='img'><img src='logistic.solution-4.png' alt='' width='700' height='433' /></div><div class='input'>  <span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m</span>)$<span class='no'>bpar</span></div><div class='output co'>#&gt;              Estimate   se_notrans   t value       Pr(&gt;t)        Lower
-#&gt; parent_0 1.057896e+02 1.9023449703 55.610119 3.768361e-16 1.016451e+02
-#&gt; kmax     6.398190e-02 0.0143201031  4.467978 3.841829e-04 3.929235e-02
-#&gt; k0       1.612775e-04 0.0005866813  0.274898 3.940351e-01 5.846688e-08
-#&gt; r        2.263946e-01 0.1718110715  1.317695 1.061044e-01 4.335843e-02
-#&gt; sigma    5.332935e+00 0.9145907310  5.830952 4.036926e-05 3.340213e+00
-#&gt;                Upper
-#&gt; parent_0 109.9341588
-#&gt; kmax       0.1041853
-#&gt; k0         0.4448749
-#&gt; r          1.1821120
-#&gt; sigma      7.3256566</div><div class='input'>  <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>m</span>)$<span class='no'>distimes</span></div><div class='output co'>#&gt;            DT50     DT90  DT50_k0 DT50_kmax
-#&gt; parent 36.86533 62.41511 4297.853  10.83349</div><div class='input'>
 </div></pre>
   </div>
   <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index d1204e2e..2f2e89d9 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -75,7 +75,7 @@ list of lists can be given in the speclist argument." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -152,7 +152,7 @@ list of lists can be given in the speclist argument.</p>
 
     <pre class="usage"><span class='fu'>mkinmod</span>(
   <span class='no'>...</span>,
-  <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>,
+  <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>,
   <span class='kw'>speclist</span> <span class='kw'>=</span> <span class='kw'>NULL</span>,
   <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>,
   <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>
@@ -252,15 +252,15 @@ in the FOCUS and NAFTA guidance documents are used.</p>
 <span class='no'>SFO_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'>mkinmod</span>(
   <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"m1"</span>),
   <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>verbose</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)</div><div class='output co'>#&gt; Compilation argument:
-#&gt;  /usr/lib/R/bin/R CMD SHLIB file66a9718e919b.c 2&gt; file66a9718e919b.c.err.txt 
+#&gt;  /usr/lib/R/bin/R CMD SHLIB fileb6a4eaab60.c 2&gt; fileb6a4eaab60.c.err.txt 
 #&gt; Program source:
 #&gt;   1: #include &lt;R.h&gt;
 #&gt;   2: 
 #&gt;   3: 
 #&gt;   4: static double parms [3];
-#&gt;   5: #define k_parent_sink parms[0]
-#&gt;   6: #define k_parent_m1 parms[1]
-#&gt;   7: #define k_m1_sink parms[2]
+#&gt;   5: #define k_parent parms[0]
+#&gt;   6: #define f_parent_to_m1 parms[1]
+#&gt;   7: #define k_m1 parms[2]
 #&gt;   8: 
 #&gt;   9: void initpar(void (* odeparms)(int *, double *)) {
 #&gt;  10:     int N = 3;
@@ -270,8 +270,8 @@ in the FOCUS and NAFTA guidance documents are used.</p>
 #&gt;  14: 
 #&gt;  15: void func ( int * n, double * t, double * y, double * f, double * rpar, int * ipar ) {
 #&gt;  16: 
-#&gt;  17: f[0] = - k_parent_sink * y[0] - k_parent_m1 * y[0];
-#&gt;  18: f[1] = + k_parent_m1 * y[0] - k_m1_sink * y[1];
+#&gt;  17: f[0] = - k_parent * y[0];
+#&gt;  18: f[1] = + f_parent_to_m1 * k_parent * y[0] - k_m1 * y[1];
 #&gt;  19: }</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'>
 <span class='co'># If we have several parallel metabolites</span>
 <span class='co'># (compare tests/testthat/test_synthetic_data_for_UBA_2014.R)</span>
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 689fb7c7..21c13156 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -74,7 +74,7 @@ kinetic parameters and initial values for the state variables." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.11</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -268,8 +268,29 @@ solver is used.</p></td>
     <pre class="examples"><div class='input'>
 <span class='no'>SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
 <span class='co'># Compare solution types</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)</span></div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)</div><div class='output co'>#&gt;    time  degradinol
+#&gt; 1     0 100.0000000
+#&gt; 2     1  74.0818221
+#&gt; 3     2  54.8811636
+#&gt; 4     3  40.6569660
+#&gt; 5     4  30.1194212
+#&gt; 6     5  22.3130160
+#&gt; 7     6  16.5298888
+#&gt; 8     7  12.2456428
+#&gt; 9     8   9.0717953
+#&gt; 10    9   6.7205513
+#&gt; 11   10   4.9787068
+#&gt; 12   11   3.6883167
+#&gt; 13   12   2.7323722
+#&gt; 14   13   2.0241911
+#&gt; 15   14   1.4995577
+#&gt; 16   15   1.1108997
+#&gt; 17   16   0.8229747
+#&gt; 18   17   0.6096747
+#&gt; 19   18   0.4516581
+#&gt; 20   19   0.3345965
+#&gt; 21   20   0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
       <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>)</div><div class='output co'>#&gt;    time  degradinol
 #&gt; 1     0 100.0000000
 #&gt; 2     1  74.0818221
@@ -291,7 +312,7 @@ solver is used.</p></td>
 #&gt; 18   17   0.6096747
 #&gt; 19   18   0.4516581
 #&gt; 20   19   0.3345965
-#&gt; 21   20   0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21   20   0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
       <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>use_compiled</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>)</div><div class='output co'>#&gt;    time  degradinol
 #&gt; 1     0 100.0000000
 #&gt; 2     1  74.0818221
@@ -313,7 +334,7 @@ solver is used.</p></td>
 #&gt; 18   17   0.6096747
 #&gt; 19   18   0.4516581
 #&gt; 20   19   0.3345965
-#&gt; 21   20   0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21   20   0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
       <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"eigen"</span>)</div><div class='output co'>#&gt;    time  degradinol
 #&gt; 1     0 100.0000000
 #&gt; 2     1  74.0818221
@@ -337,25 +358,26 @@ solver is used.</p></td>
 #&gt; 20   19   0.3345965
 #&gt; 21   20   0.2478752</div><div class='input'>
 <span class='co'># Compare integration methods to analytical solution</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
-      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt; <span class='error'>Error in (function (t, parent_0, k) {    parent = parent_0 * exp(-k * t)})(t = 0:20, parent.0 = c(degradinol = 100), k = 0.3): unbenutztes Argument (parent.0 = 100)</span></div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+      <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
+#&gt; 21   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
       <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"lsoda"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
-#&gt; 21   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
       <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"ode45"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
-#&gt; 21   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
+#&gt; 21   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>), <span class='fl'>0</span>:<span class='fl'>20</span>,
       <span class='kw'>method</span> <span class='kw'>=</span> <span class='st'>"rk4"</span>)[<span class='fl'>21</span>,]</div><div class='output co'>#&gt;    time degradinol
 #&gt; 21   20  0.2480043</div><div class='input'><span class='co'># rk4 is not as precise here</span>
 
 <span class='co'># The number of output times used to make a lot of difference until the</span>
 <span class='co'># default for atol was adjusted</span>
-<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+<span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
       <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>))[<span class='fl'>201</span>,]</div><div class='output co'>#&gt;     time degradinol
-#&gt; 201   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol_sink</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
+#&gt; 201   20  0.2478752</div><div class='input'><span class='fu'>mkinpredict</span>(<span class='no'>SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_degradinol</span> <span class='kw'>=</span> <span class='fl'>0.3</span>), <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>degradinol</span> <span class='kw'>=</span> <span class='fl'>100</span>),
       <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.01</span>))[<span class='fl'>2001</span>,]</div><div class='output co'>#&gt;      time degradinol
 #&gt; 2001   20  0.2478752</div><div class='input'>
 <span class='co'># Check compiled model versions - they are faster than the eigenvalue based solutions!</span>
 <span class='no'>SFO_SFO</span> <span class='kw'>=</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>, <span class='kw'>to</span> <span class='kw'>=</span> <span class='st'>"m1"</span>),
-                  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
+                  <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='kw'>type</span> <span class='kw'>=</span> <span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>)</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'><span class='kw'>if</span>(<span class='fu'><a href='https://rdrr.io/r/base/library.html'>require</a></span>(<span class='no'>rbenchmark</span>)) {
   <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(
     <span class='kw'>eigen</span> <span class='kw'>=</span> <span class='fu'>mkinpredict</span>(<span class='no'>SFO_SFO</span>, <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_m1</span> <span class='kw'>=</span> <span class='fl'>0.05</span>, <span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>, <span class='kw'>k_m1_sink</span> <span class='kw'>=</span> <span class='fl'>0.01</span>),
       <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>100</span>, <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fl'>0</span>), <span class='fu'><a href='https://rdrr.io/r/base/seq.html'>seq</a></span>(<span class='fl'>0</span>, <span class='fl'>20</span>, <span class='kw'>by</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
@@ -371,7 +393,7 @@ solver is used.</p></td>
 }</div><div class='output co'>#&gt; <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#&gt;               test replications elapsed relative user.self sys.self user.child
 #&gt; 3          deSolve           10   0.229   28.625     0.229        0          0
 #&gt; 2 deSolve_compiled           10   0.008    1.000     0.008        0          0
-#&gt; 1            eigen           10   0.025    3.125     0.026        0          0
+#&gt; 1            eigen           10   0.026    3.250     0.025        0          0
 #&gt;   sys.child
 #&gt; 3         0
 #&gt; 2         0
diff --git a/docs/reference/nlme-1.png b/docs/reference/nlme-1.png
index 68ccb43f..8db1f999 100644
--- a/docs/reference/nlme-1.png
+++ b/docs/reference/nlme-1.png
diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html
index 70c6b63c..b92d2141 100644
--- a/docs/reference/nlme.html
+++ b/docs/reference/nlme.html
@@ -10,23 +10,27 @@
 
 
 <!-- jquery -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/jquery/3.4.1/jquery.min.js" integrity="sha256-CSXorXvZcTkaix6Yvo6HppcZGetbYMGWSFlBw8HfCJo=" crossorigin="anonymous"></script>
 <!-- Bootstrap -->
 
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/css/bootstrap.min.css" integrity="sha256-916EbMg70RQy9LHiGkXzG8hSg9EdNy97GazNG/aiY1w=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/css/bootstrap.min.css" integrity="sha256-bZLfwXAP04zRMK2BjiO8iu9pf4FbLqX6zitd+tIvLhE=" crossorigin="anonymous" />
 
-<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.3.7/js/bootstrap.min.js" integrity="sha256-U5ZEeKfGNOja007MMD3YBI0A3OSZOQbeG6z2f2Y0hu8=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/3.4.1/js/bootstrap.min.js" integrity="sha256-nuL8/2cJ5NDSSwnKD8VqreErSWHtnEP9E7AySL+1ev4=" crossorigin="anonymous"></script>
+
+<!-- bootstrap-toc -->
+<link rel="stylesheet" href="../bootstrap-toc.css">
+<script src="../bootstrap-toc.js"></script>
 
 <!-- Font Awesome icons -->
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/all.min.css" integrity="sha256-nAmazAk6vS34Xqo0BSrTb+abbtFlgsFK7NKSi6o7Y78=" crossorigin="anonymous" />
-<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.7.1/css/v4-shims.min.css" integrity="sha256-6qHlizsOWFskGlwVOKuns+D1nB6ssZrHQrNj1wGplHc=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/all.min.css" integrity="sha256-mmgLkCYLUQbXn0B1SRqzHar6dCnv9oZFPEC1g1cwlkk=" crossorigin="anonymous" />
+<link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/font-awesome/5.12.1/css/v4-shims.min.css" integrity="sha256-wZjR52fzng1pJHwx4aV2AO3yyTOXrcDW7jBpJtTwVxw=" crossorigin="anonymous" />
 
 <!-- clipboard.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.4/clipboard.min.js" integrity="sha256-FiZwavyI2V6+EXO1U+xzLG3IKldpiTFf3153ea9zikQ=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/clipboard.js/2.0.6/clipboard.min.js" integrity="sha256-inc5kl9MA1hkeYUt+EC3BhlIgyp/2jDIyBLS6k3UxPI=" crossorigin="anonymous"></script>
 
 <!-- headroom.js -->
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/headroom.min.js" integrity="sha256-DJFC1kqIhelURkuza0AvYal5RxMtpzLjFhsnVIeuk+U=" crossorigin="anonymous"></script>
-<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.9.4/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/headroom.min.js" integrity="sha256-AsUX4SJE1+yuDu5+mAVzJbuYNPHj/WroHuZ8Ir/CkE0=" crossorigin="anonymous"></script>
+<script src="https://cdnjs.cloudflare.com/ajax/libs/headroom/0.11.0/jQuery.headroom.min.js" integrity="sha256-ZX/yNShbjqsohH1k95liqY9Gd8uOiE1S4vZc+9KQ1K4=" crossorigin="anonymous"></script>
 
 <!-- pkgdown -->
 <link href="../pkgdown.css" rel="stylesheet">
@@ -40,7 +44,6 @@
 an mmkin row object. An mmkin row object is essentially a list of mkinfit
 objects that have been obtained by fitting the same model to a list of
 datasets." />
-<meta name="twitter:card" content="summary" />
 
 
 
@@ -58,7 +61,7 @@ datasets." />
 
   </head>
 
-  <body>
+  <body data-spy="scroll" data-target="#toc">
     <div class="container template-reference-topic">
       <header>
       <div class="navbar navbar-default navbar-fixed-top" role="navigation">
@@ -72,7 +75,7 @@ datasets." />
       </button>
       <span class="navbar-brand">
         <a class="navbar-link" href="../index.html">mkin</a>
-        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span>
+        <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
       </span>
     </div>
 
@@ -116,7 +119,12 @@ datasets." />
 </li>
       </ul>
       <ul class="nav navbar-nav navbar-right">
-        
+        <li>
+  <a href="http://github.com/jranke/mkin/">
+    <span class="fab fa fab fa-github fa-lg"></span>
+     
+  </a>
+</li>
       </ul>
       
     </div><!--/.nav-collapse -->
@@ -131,7 +139,7 @@ datasets." />
   <div class="col-md-9 contents">
     <div class="page-header">
     <h1>Helper functions to create nlme models from mmkin row objects</h1>
-    
+    <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.R'><code>R/nlme.R</code></a></small>
     <div class="hidden name"><code>nlme.Rd</code></div>
     </div>
 
@@ -177,15 +185,15 @@ datasets.</p>
     <pre class="examples"><div class='input'><span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>)
 <span class='no'>m_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))
 <span class='no'>d_SFO_1</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>,
-  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
+  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.1</span>),
   <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>98</span>), <span class='no'>sampling_times</span>)
 <span class='no'>d_SFO_1_long</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_1</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
 <span class='no'>d_SFO_2</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>,
-  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.05</span>),
+  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.05</span>),
   <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>102</span>), <span class='no'>sampling_times</span>)
 <span class='no'>d_SFO_2_long</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_2</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
 <span class='no'>d_SFO_3</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>,
-  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
+  <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent</span> <span class='kw'>=</span> <span class='fl'>0.02</span>),
   <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>103</span>), <span class='no'>sampling_times</span>)
 <span class='no'>d_SFO_3_long</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_3</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>)
 
@@ -214,42 +222,37 @@ datasets.</p>
 #&gt;   Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) 
 #&gt;  Data: grouped_data 
 #&gt;        AIC      BIC    logLik
-#&gt;   298.2781 307.7372 -144.1391
+#&gt;   252.7798 262.1358 -121.3899
 #&gt; 
 #&gt; Random effects:
 #&gt;  Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1)
 #&gt;  Level: ds
 #&gt;  Structure: Diagonal
-#&gt;          parent_0 log_k_parent_sink Residual
-#&gt; StdDev: 0.9374733         0.7098105  3.83543
+#&gt;             parent_0 log_k_parent_sink Residual
+#&gt; StdDev: 0.0006768135         0.6800777 2.489397
 #&gt; 
 #&gt; Fixed effects: parent_0 + log_k_parent_sink ~ 1 
-#&gt;                       Value Std.Error DF  t-value p-value
-#&gt; parent_0          101.76838 1.1445444 45 88.91606       0
-#&gt; log_k_parent_sink  -3.05444 0.4195622 45 -7.28008       0
+#&gt;                       Value Std.Error DF   t-value p-value
+#&gt; parent_0          101.74884 0.6456014 44 157.60321       0
+#&gt; log_k_parent_sink  -3.05575 0.4015811 44  -7.60929       0
 #&gt;  Correlation: 
 #&gt;                   prnt_0
-#&gt; log_k_parent_sink 0.034 
+#&gt; log_k_parent_sink 0.026 
 #&gt; 
 #&gt; Standardized Within-Group Residuals:
 #&gt;        Min         Q1        Med         Q3        Max 
-#&gt; -2.6169360 -0.2185329  0.0574070  0.5720937  3.0459868 
+#&gt; -2.1317488 -0.6878121  0.0828385  0.8592270  2.9529864 
 #&gt; 
-#&gt; Number of Observations: 49
-#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.html'>plot</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span>(<span class='no'>m_nlme</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0</span>:<span class='fl'>1</span>), <span class='kw'>layout</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>1</span>))</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'># augPred does not seem to work on fits with more than one state
+#&gt; Number of Observations: 48
+#&gt; Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span>(<span class='no'>m_nlme</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0</span>:<span class='fl'>1</span>), <span class='kw'>layout</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>1</span>))</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'># augPred does not seem to work on fits with more than one state
 # variable
 
 </div></pre>
   </div>
-  <div class="col-md-3 hidden-xs hidden-sm" id="sidebar">
-    <h2>Contents</h2>
-    <ul class="nav nav-pills nav-stacked">
-      <li><a href="#arguments">Arguments</a></li>
-      <li><a href="#value">Value</a></li>
-      <li><a href="#see-also">See also</a></li>
-      <li><a href="#examples">Examples</a></li>
-    </ul>
-
+  <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar">
+    <nav id="toc" data-toggle="toc" class="sticky-top">
+      <h2 data-toc-skip>Contents</h2>
+    </nav>
   </div>
 </div>
 
@@ -260,7 +263,7 @@ datasets.</p>
 </div>
 
 <div class="pkgdown">
-  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.4.1.</p>
+  <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p>
 </div>
 
       </footer>
diff --git a/docs/sitemap.xml b/docs/sitemap.xml
index 5abcc894..81368436 100644
--- a/docs/sitemap.xml
+++ b/docs/sitemap.xml
@@ -61,6 +61,9 @@
     <loc>https://pkgdown.jrwb.de/mkin/reference/confint.mkinfit.html</loc>
   </url>
   <url>
+    <loc>https://pkgdown.jrwb.de/mkin/reference/create_deg_func.html</loc>
+  </url>
+  <url>
     <loc>https://pkgdown.jrwb.de/mkin/reference/endpoints.html</loc>
   </url>
   <url>
diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd
index 343f83f0..f72df23b 100644
--- a/man/HS.solution.Rd
+++ b/man/HS.solution.Rd
@@ -7,10 +7,21 @@
 HS.solution(t, parent_0, k1, k2, tb)
 }
 \arguments{
+\item{t}{Time.}
+
+\item{parent_0}{Starting value for the response variable at time zero.}
+
+\item{k1}{First kinetic constant.}
+
+\item{k2}{Second kinetic constant.}
+
 \item{tb}{Break point. Before this time, exponential decline according to
 \code{k1} is calculated, after this time, exponential decline proceeds
 according to \code{k2}.}
 }
+\value{
+The value of the response variable at time \code{t}.
+}
 \description{
 Function describing two exponential decline functions with a break point
 between them.
@@ -20,6 +31,18 @@ between them.
   plot(function(x) HS.solution(x, 100, 2, 0.3, 0.5), 0, 2, ylim=c(0,100))
 
 }
+\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}
+FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
+  \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
 \seealso{
 Other parent solutions: 
 \code{\link{DFOP.solution}()},
diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd
index c70ce13b..98a8c684 100644
--- a/man/SFORB.solution.Rd
+++ b/man/SFORB.solution.Rd
@@ -7,6 +7,10 @@
 SFORB.solution(t, parent_0, k_12, k_21, k_1output)
 }
 \arguments{
+\item{t}{Time.}
+
+\item{parent_0}{Starting value for the response variable at time zero.}
+
 \item{k_12}{Kinetic constant describing transfer from free to bound.}
 
 \item{k_21}{Kinetic constant describing transfer from bound to free.}
@@ -30,6 +34,18 @@ and no substance in the bound fraction.
   \dontrun{plot(function(x) SFORB.solution(x, 100, 0.5, 2, 3), 0, 2)}
 
 }
+\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}
+FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
+  and Degradation Kinetics from Environmental Fate Studies on Pesticides in
+  EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
+  Version 1.1, 18 December 2014
+  \url{http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics}
+}
 \seealso{
 Other parent solutions: 
 \code{\link{DFOP.solution}()},
diff --git a/man/create_deg_func.Rd b/man/create_deg_func.Rd
new file mode 100644
index 00000000..2eefdb80
--- /dev/null
+++ b/man/create_deg_func.Rd
@@ -0,0 +1,26 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/create_deg_func.R
+\name{create_deg_func}
+\alias{create_deg_func}
+\title{Create degradation functions for known analytical solutions}
+\usage{
+create_deg_func(spec, use_of_ff = c("min", "max"))
+}
+\arguments{
+\item{spec}{List of model specifications as contained in mkinmod objects}
+
+\item{use_of_ff}{Minimum or maximum use of formation fractions}
+}
+\value{
+Degradation function to be attached to mkinmod objects
+}
+\description{
+Create degradation functions for known analytical solutions
+}
+\examples{
+
+SFO_SFO <- mkinmod(
+  parent = mkinsub("SFO", "m1"),
+  m1 = mkinsub("SFO"))
+fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+}
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 589ee8ec..33b3d44a 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -1,12 +1,10 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/logistic.solution.R, R/parent_solutions.R
+% Please edit documentation in R/parent_solutions.R
 \name{logistic.solution}
 \alias{logistic.solution}
 \title{Logistic kinetics}
 \usage{
 logistic.solution(t, parent_0, kmax, k0, r)
-
-logistic.solution(t, parent_0, kmax, k0, r)
 }
 \arguments{
 \item{t}{Time.}
@@ -18,8 +16,6 @@ logistic.solution(t, parent_0, kmax, k0, r)
 \item{k0}{Minumum rate constant effective at time zero.}
 
 \item{r}{Growth rate of the increase in the rate constant.}
-
-\item{parent.0}{Starting value for the response variable at time zero.}
 }
 \value{
 The value of the response variable at time \code{t}.
@@ -27,16 +23,10 @@ The value of the response variable at time \code{t}.
 \description{
 Function describing exponential decline from a defined starting value, with
 an increasing rate constant, supposedly caused by microbial growth
-
-Function describing exponential decline from a defined starting value, with
-an increasing rate constant, supposedly caused by microbial growth
 }
 \note{
 The solution of the logistic model reduces to the
   \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.
-
-The solution of the logistic model reduces to the
-  \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}.
 }
 \examples{
 
@@ -74,43 +64,13 @@ The solution of the logistic model reduces to the
   summary(m)$bpar
   endpoints(m)$distimes
 
-
-  # Reproduce the plot on page 57 of FOCUS (2014)
-  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.2),
-       from = 0, to = 100, ylim = c(0, 100),
-       xlab = "Time", ylab = "Residue")
-  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.4),
-       from = 0, to = 100, add = TRUE, lty = 2, col = 2)
-  plot(function(x) logistic.solution(x, 100, 0.08, 0.0001, 0.8),
-       from = 0, to = 100, add = TRUE, lty = 3, col = 3)
-  plot(function(x) logistic.solution(x, 100, 0.08, 0.001, 0.2),
-       from = 0, to = 100, add = TRUE, lty = 4, col = 4)
-  plot(function(x) logistic.solution(x, 100, 0.08, 0.08, 0.2),
-       from = 0, to = 100, add = TRUE, lty = 5, col = 5)
-  legend("topright", inset = 0.05,
-         legend = paste0("k0 = ", c(0.0001, 0.0001, 0.0001, 0.001, 0.08),
-                         ", r = ", c(0.2, 0.4, 0.8, 0.2, 0.2)),
-         lty = 1:5, col = 1:5)
-
-  # Fit with synthetic data
-  logistic <- mkinmod(parent = mkinsub("logistic"))
-
-  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
-  parms_logistic <- c(kmax = 0.08, k0 = 0.0001, r = 0.2)
-  d_logistic <- mkinpredict(logistic,
-    parms_logistic, c(parent = 100),
-    sampling_times)
-  d_2_1 <- add_err(d_logistic,
-    sdfunc = function(x) sigma_twocomp(x, 0.5, 0.07),
-    n = 1, reps = 2, digits = 5, LOD = 0.1, seed = 123456)[[1]]
-
-  m <- mkinfit("logistic", d_2_1, quiet = TRUE)
-  plot_sep(m)
-  summary(m)$bpar
-  endpoints(m)$distimes
-
 }
 \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}
 FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence
   and Degradation Kinetics from Environmental Fate Studies on Pesticides in
   EU Registration} Report of the FOCUS Work Group on Degradation Kinetics,
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 020917b9..2ba917d6 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -6,7 +6,7 @@
 \usage{
 mkinmod(
   ...,
-  use_of_ff = "min",
+  use_of_ff = "max",
   speclist = NULL,
   quiet = FALSE,
   verbose = FALSE
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 366d5b83..f7e4acfc 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -102,36 +102,36 @@ kinetic parameters and initial values for the state variables.
 
 SFO <- mkinmod(degradinol = mkinsub("SFO"))
 # Compare solution types
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "analytical")
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "deSolve")
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "deSolve", use_compiled = FALSE)
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "eigen")
 
 # Compare integration methods to analytical solution
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       solution_type = "analytical")[21,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       method = "lsoda")[21,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       method = "ode45")[21,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100), 0:20,
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100), 0:20,
       method = "rk4")[21,]
 # rk4 is not as precise here
 
 # The number of output times used to make a lot of difference until the
 # default for atol was adjusted
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
       seq(0, 20, by = 0.1))[201,]
-mkinpredict(SFO, c(k_degradinol_sink = 0.3), c(degradinol = 100),
+mkinpredict(SFO, c(k_degradinol = 0.3), c(degradinol = 100),
       seq(0, 20, by = 0.01))[2001,]
 
 # Check compiled model versions - they are faster than the eigenvalue based solutions!
 SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),
-                  m1 = list(type = "SFO"))
+                  m1 = list(type = "SFO"), use_of_ff = "min")
 if(require(rbenchmark)) {
   benchmark(
     eigen = mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
diff --git a/man/nlme.Rd b/man/nlme.Rd
index 4a668ac0..a9e368dd 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -37,15 +37,15 @@ datasets.
 sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
 m_SFO <- mkinmod(parent = mkinsub("SFO"))
 d_SFO_1 <- mkinpredict(m_SFO,
-  c(k_parent_sink = 0.1),
+  c(k_parent = 0.1),
   c(parent = 98), sampling_times)
 d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
 d_SFO_2 <- mkinpredict(m_SFO,
-  c(k_parent_sink = 0.05),
+  c(k_parent = 0.05),
   c(parent = 102), sampling_times)
 d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
 d_SFO_3 <- mkinpredict(m_SFO,
-  c(k_parent_sink = 0.02),
+  c(k_parent = 0.02),
   c(parent = 103), sampling_times)
 d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
 
diff --git a/test.log b/test.log
index b57bd69a..72ed4ee3 100644
--- a/test.log
+++ b/test.log
@@ -2,34 +2,34 @@ Loading mkin
 Testing mkin
 ✔ |  OK F W S | Context
 ✔ |   2       | Export dataset for reading into CAKE
-✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.6 s]
+✔ |  13       | Results for FOCUS D established in expertise for UBA (Ranke 2014) [3.7 s]
 ✔ |   4       | Calculation of FOCUS chi2 error levels [2.2 s]
-✔ |   6       | Fitting the SFORB model [9.1 s]
+✔ |   7       | Fitting the SFORB model [11.7 s]
 ✔ |   5       | Calculation of Akaike weights
-✔ |  10       | Confidence intervals and p-values [9.6 s]
-✔ |  14       | Error model fitting [38.5 s]
+✔ |  10       | Confidence intervals and p-values [9.3 s]
+✔ |  14       | Error model fitting [37.6 s]
 ✔ |   6       | Test fitting the decline of metabolites from their maximum [0.8 s]
 ✔ |   1       | Fitting the logistic model [0.8 s]
 ✔ |   1       | Test dataset class mkinds used in gmkin
-✔ |  12       | Special cases of mkinfit calls [2.3 s]
+✔ |  12       | Special cases of mkinfit calls [2.2 s]
 ✔ |   8       | mkinmod model generation and printing [0.2 s]
 ✔ |   3       | Model predictions with mkinpredict [0.4 s]
-✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.2 s]
-✔ |   9       | Nonlinear mixed-effects models [12.3 s]
+✔ |  16       | Evaluations according to 2015 NAFTA guidance [4.1 s]
+✔ |   9       | Nonlinear mixed-effects models [12.0 s]
 ✔ |   4       | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
 ✔ |   3       | Summary
-✔ |  14       | Plotting [5.1 s]
+✔ |  14       | Plotting [4.9 s]
 ✔ |   4       | AIC calculation
 ✔ |   4       | Residuals extracted from mkinfit models
 ✔ |   2       | Complex test case from Schaefer et al. (2007) Piacenza paper [5.3 s]
 ✔ |   1       | Summaries of old mkinfit objects
 ✔ |   4       | Results for synthetic data established in expertise for UBA (Ranke 2014) [7.2 s]
-✔ |   9       | Hypothesis tests [38.2 s]
+✔ |   9       | Hypothesis tests [37.9 s]
 
 ══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 142.5 s
+Duration: 143.0 s
 
-OK:       155
+OK:       156
 Failed:   0
 Warnings: 0
 Skipped:  0
diff --git a/tests/testthat/FOCUS_2006_D.csf b/tests/testthat/FOCUS_2006_D.csf
index fa96de74..7c29ab46 100644
--- a/tests/testthat/FOCUS_2006_D.csf
+++ b/tests/testthat/FOCUS_2006_D.csf
@@ -5,7 +5,7 @@ Description:
 MeasurementUnits: % AR
 TimeUnits: days
 Comments: Created using mkin::CAKE_export
-Date: 2020-05-06
+Date: 2020-05-07
 Optimiser: IRLS
 
 [Data]
diff --git a/tests/testthat/SFO_SFO_printed.txt b/tests/testthat/SFO_SFO_printed.txt
index d0402fc0..a3a04be2 100644
--- a/tests/testthat/SFO_SFO_printed.txt
+++ b/tests/testthat/SFO_SFO_printed.txt
@@ -1,5 +1,5 @@
 <mkinmod> model generated with
-Use of formation fractions $use_of_ff: min 
+Use of formation fractions $use_of_ff: max 
 Specification $spec:
 $parent
 $type: SFO; $to: m1; $sink: TRUE
@@ -7,5 +7,5 @@ $m1
 $type: SFO; $sink: TRUE
 Coefficient matrix $coefmat available
 Differential equations:
-d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+d_parent/dt = - k_parent * parent
+d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
diff --git a/tests/testthat/summary_DFOP_FOCUS_C.txt b/tests/testthat/summary_DFOP_FOCUS_C.txt
index 14e00f62..4f96c8d3 100644
--- a/tests/testthat/summary_DFOP_FOCUS_C.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_C.txt
@@ -33,6 +33,11 @@ g_ilr     0.000000  -Inf   Inf
 Fixed parameter values:
 None
 
+Results:
+
+       AIC      BIC    logLik
+  29.02372 30.00984 -9.511861
+
 Optimised, transformed parameters with symmetric confidence intervals:
          Estimate Std. Error   Lower   Upper
 parent_0  85.0000    0.66620 83.1500 86.8500
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
index 66ab9348..fe697794 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_deSolve.txt
@@ -4,8 +4,8 @@ Date of fit:     Dummy date for testing
 Date of summary: Dummy date for testing 
 
 Equations:
-d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+d_parent/dt = - k_parent * parent
+d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
 
 Model predictions using solution type deSolve 
 
@@ -16,30 +16,35 @@ Error model: Constant variance
 Error model algorithm: OLS 
 
 Starting values for parameters to be optimised:
-                 value   type
-parent_0      100.7500  state
-k_parent_sink   0.1000 deparm
-k_parent_m1     0.1001 deparm
-k_m1_sink       0.1002 deparm
+                  value   type
+parent_0       100.7500  state
+k_parent         0.1000 deparm
+k_m1             0.1001 deparm
+f_parent_to_m1   0.5000 deparm
 
 Starting values for the transformed parameters actually optimised:
-                       value lower upper
-parent_0          100.750000  -Inf   Inf
-log_k_parent_sink  -2.302585  -Inf   Inf
-log_k_parent_m1    -2.301586  -Inf   Inf
-log_k_m1_sink      -2.300587  -Inf   Inf
+                    value lower upper
+parent_0       100.750000  -Inf   Inf
+log_k_parent    -2.302585  -Inf   Inf
+log_k_m1        -2.301586  -Inf   Inf
+f_parent_ilr_1   0.000000  -Inf   Inf
 
 Fixed parameter values:
      value  type
 m1_0     0 state
 
+Results:
+
+       AIC      BIC    logLik
+  204.4486 212.6365 -97.22429
+
 Optimised, transformed parameters with symmetric confidence intervals:
-                  Estimate Std. Error  Lower   Upper
-parent_0            99.600    1.57000 96.400 102.800
-log_k_parent_sink   -3.038    0.07626 -3.193  -2.883
-log_k_parent_m1     -2.980    0.04033 -3.062  -2.898
-log_k_m1_sink       -5.248    0.13320 -5.518  -4.977
-sigma                3.126    0.35850  2.396   3.855
+               Estimate Std. Error    Lower    Upper
+parent_0       99.60000    1.57000 96.40000 102.8000
+log_k_parent   -2.31600    0.04087 -2.39900  -2.2330
+log_k_m1       -5.24800    0.13320 -5.51800  -4.9770
+f_parent_ilr_1  0.04096    0.06312 -0.08746   0.1694
+sigma           3.12600    0.35850  2.39600   3.8550
 
 Parameter correlation:
 NULL
@@ -48,24 +53,23 @@ Backtransformed parameters:
 Confidence intervals for internally transformed parameters are asymmetric.
 t-test (unrealistically) based on the assumption of normal distribution
 for estimators of untransformed parameters.
-               Estimate t value    Pr(>t)     Lower     Upper
-parent_0      99.600000  63.430 2.298e-36 96.400000 1.028e+02
-k_parent_sink  0.047920  13.110 6.126e-15  0.041030 5.596e-02
-k_parent_m1    0.050780  24.800 3.269e-23  0.046780 5.512e-02
-k_m1_sink      0.005261   7.510 6.165e-09  0.004012 6.898e-03
-sigma          3.126000   8.718 2.235e-10  2.396000 3.855e+00
+                Estimate t value    Pr(>t)     Lower     Upper
+parent_0       99.600000  63.430 2.298e-36 96.400000 1.028e+02
+k_parent        0.098700  24.470 4.955e-23  0.090820 1.073e-01
+k_m1            0.005261   7.510 6.165e-09  0.004012 6.898e-03
+f_parent_to_m1  0.514500  23.070 3.104e-22  0.469100 5.596e-01
+sigma           3.126000   8.718 2.235e-10  2.396000 3.855e+00
 
 FOCUS Chi2 error levels in percent:
          err.min n.optim df
 All data   6.398       4 15
-parent     6.827       3  6
-m1         4.490       1  9
+parent     6.459       2  7
+m1         4.690       2  8
 
 Resulting formation fractions:
                 ff
-parent_sink 0.4855
 parent_m1   0.5145
-m1_sink     1.0000
+parent_sink 0.4855
 
 Estimated disappearance times:
           DT50   DT90
@@ -78,10 +82,10 @@ Data:
     0   parent   102.04  99.59848  2.442e+00
     1   parent    93.50  90.23787  3.262e+00
     1   parent    92.50  90.23787  2.262e+00
-    3   parent    63.23  74.07320 -1.084e+01
-    3   parent    68.99  74.07320 -5.083e+00
-    7   parent    52.32  49.91207  2.408e+00
-    7   parent    55.13  49.91207  5.218e+00
+    3   parent    63.23  74.07319 -1.084e+01
+    3   parent    68.99  74.07319 -5.083e+00
+    7   parent    52.32  49.91206  2.408e+00
+    7   parent    55.13  49.91206  5.218e+00
    14   parent    27.27  25.01257  2.257e+00
    14   parent    26.64  25.01257  1.627e+00
    21   parent    11.50  12.53462 -1.035e+00
@@ -91,7 +95,7 @@ Data:
    50   parent     0.69   0.71624 -2.624e-02
    50   parent     0.63   0.71624 -8.624e-02
    75   parent     0.05   0.06074 -1.074e-02
-   75   parent     0.06   0.06074 -7.382e-04
+   75   parent     0.06   0.06074 -7.381e-04
     1       m1     4.84   4.80296  3.704e-02
     1       m1     5.64   4.80296  8.370e-01
     3       m1    12.91  13.02400 -1.140e-01
diff --git a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
index 1626c5da..6ddbc1ab 100644
--- a/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
+++ b/tests/testthat/summary_DFOP_FOCUS_D_eigen.txt
@@ -4,8 +4,8 @@ Date of fit:     Dummy date for testing
 Date of summary: Dummy date for testing 
 
 Equations:
-d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
+d_parent/dt = - k_parent * parent
+d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
 
 Model predictions using solution type eigen 
 
@@ -16,30 +16,35 @@ Error model: Constant variance
 Error model algorithm: OLS 
 
 Starting values for parameters to be optimised:
-                 value   type
-parent_0      100.7500  state
-k_parent_sink   0.1000 deparm
-k_parent_m1     0.1001 deparm
-k_m1_sink       0.1002 deparm
+                  value   type
+parent_0       100.7500  state
+k_parent         0.1000 deparm
+k_m1             0.1001 deparm
+f_parent_to_m1   0.5000 deparm
 
 Starting values for the transformed parameters actually optimised:
-                       value lower upper
-parent_0          100.750000  -Inf   Inf
-log_k_parent_sink  -2.302585  -Inf   Inf
-log_k_parent_m1    -2.301586  -Inf   Inf
-log_k_m1_sink      -2.300587  -Inf   Inf
+                    value lower upper
+parent_0       100.750000  -Inf   Inf
+log_k_parent    -2.302585  -Inf   Inf
+log_k_m1        -2.301586  -Inf   Inf
+f_parent_ilr_1   0.000000  -Inf   Inf
 
 Fixed parameter values:
      value  type
 m1_0     0 state
 
+Results:
+
+       AIC      BIC    logLik
+  204.4486 212.6365 -97.22429
+
 Optimised, transformed parameters with symmetric confidence intervals:
-                  Estimate Std. Error  Lower   Upper
-parent_0            99.600    1.57000 96.400 102.800
-log_k_parent_sink   -3.038    0.07626 -3.193  -2.883
-log_k_parent_m1     -2.980    0.04033 -3.062  -2.898
-log_k_m1_sink       -5.248    0.13320 -5.518  -4.977
-sigma                3.126    0.35850  2.396   3.855
+               Estimate Std. Error    Lower    Upper
+parent_0       99.60000    1.57000 96.40000 102.8000
+log_k_parent   -2.31600    0.04087 -2.39900  -2.2330
+log_k_m1       -5.24800    0.13320 -5.51800  -4.9770
+f_parent_ilr_1  0.04096    0.06312 -0.08746   0.1694
+sigma           3.12600    0.35850  2.39600   3.8550
 
 Parameter correlation:
 NULL
@@ -48,24 +53,23 @@ Backtransformed parameters:
 Confidence intervals for internally transformed parameters are asymmetric.
 t-test (unrealistically) based on the assumption of normal distribution
 for estimators of untransformed parameters.
-               Estimate t value    Pr(>t)     Lower     Upper
-parent_0      99.600000  63.430 2.298e-36 96.400000 1.028e+02
-k_parent_sink  0.047920  13.110 6.126e-15  0.041030 5.596e-02
-k_parent_m1    0.050780  24.800 3.269e-23  0.046780 5.512e-02
-k_m1_sink      0.005261   7.510 6.165e-09  0.004012 6.898e-03
-sigma          3.126000   8.718 2.235e-10  2.396000 3.855e+00
+                Estimate t value    Pr(>t)     Lower     Upper
+parent_0       99.600000  63.430 2.298e-36 96.400000 1.028e+02
+k_parent        0.098700  24.470 4.955e-23  0.090820 1.073e-01
+k_m1            0.005261   7.510 6.165e-09  0.004012 6.898e-03
+f_parent_to_m1  0.514500  23.070 3.104e-22  0.469100 5.596e-01
+sigma           3.126000   8.718 2.235e-10  2.396000 3.855e+00
 
 FOCUS Chi2 error levels in percent:
          err.min n.optim df
 All data   6.398       4 15
-parent     6.827       3  6
-m1         4.490       1  9
+parent     6.459       2  7
+m1         4.690       2  8
 
 Resulting formation fractions:
                 ff
-parent_sink 0.4855
 parent_m1   0.5145
-m1_sink     1.0000
+parent_sink 0.4855
 
 Estimated disappearance times:
           DT50   DT90
diff --git a/tests/testthat/test_SFORB.R b/tests/testthat/test_SFORB.R
index ad9881a8..4fb736ec 100644
--- a/tests/testthat/test_SFORB.R
+++ b/tests/testthat/test_SFORB.R
@@ -15,16 +15,20 @@ test_that("Fitting the SFORB model is equivalent to fitting DFOP", {
     use_of_ff = "max", quiet = TRUE)
   SFORB_SFO <- mkinmod(parent = mkinsub("SFORB", "M1"),
     M1 = mkinsub("SFO"),
+    use_of_ff = "min", quiet = TRUE)
+  SFORB_SFO_ff <- mkinmod(parent = mkinsub("SFORB", "M1"),
+    M1 = mkinsub("SFO"),
     use_of_ff = "max", quiet = TRUE)
 
-  SFORB_SFO$coefmat
-
   f_dfop_sfo <- mkinfit(DFOP_SFO, DFOP_par_c, quiet = TRUE)
   f_sforb_sfo <- mkinfit(SFORB_SFO, DFOP_par_c, quiet = TRUE)
+  f_sforb_sfo_ff <- mkinfit(SFORB_SFO_ff, DFOP_par_c, quiet = TRUE)
   f_sforb_sfo_eigen <- mkinfit(SFORB_SFO, DFOP_par_c, solution_type = "eigen", quiet = TRUE)
 
   expect_equivalent(endpoints(f_sforb_sfo)$distimes, endpoints(f_dfop_sfo)$distimes,
     tolerance = 1e-6)
+  expect_equivalent(endpoints(f_sforb_sfo_ff)$distimes, endpoints(f_dfop_sfo)$distimes,
+    tolerance = 1e-6)
   expect_equivalent(endpoints(f_sforb_sfo_eigen)$distimes, endpoints(f_dfop_sfo)$distimes,
     tolerance = 1e-6)
 })
diff --git a/tests/testthat/test_nlme.R b/tests/testthat/test_nlme.R
index e5e19c60..31fb19de 100644
--- a/tests/testthat/test_nlme.R
+++ b/tests/testthat/test_nlme.R
@@ -2,20 +2,21 @@ context("Nonlinear mixed-effects models")
 
 library(nlme)
 
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+
 test_that("nlme_function works correctly", {
 
-  sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
   m_SFO <- mkinmod(parent = mkinsub("SFO"))
   d_SFO_1 <- mkinpredict(m_SFO,
-    c(k_parent_sink = 0.1),
+    c(k_parent = 0.1),
     c(parent = 98), sampling_times)
   d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
   d_SFO_2 <- mkinpredict(m_SFO,
-    c(k_parent_sink = 0.05),
+    c(k_parent = 0.05),
     c(parent = 102), sampling_times)
   d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
   d_SFO_3 <- mkinpredict(m_SFO,
-    c(k_parent_sink = 0.02),
+    c(k_parent = 0.02),
     c(parent = 103), sampling_times)
   d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
 
@@ -33,7 +34,6 @@ test_that("nlme_function works correctly", {
   # The following assignment was introduced for nlme as evaluated by testthat
   # to find the function
   assign("nlme_f", nlme_f, pos = globalenv())
-  assign("sampling_times", sampling_times, pos = globalenv())
 
   m_nlme_raw <- nlme(value ~ SSasymp(time, 0, parent_0, log_k_parent_sink),
     data = grouped_data,
@@ -101,7 +101,7 @@ test_that("nlme_function works correctly in other cases", {
   SFO <- mkinmod(parent = mkinsub("SFO"))
   pred_sfo <- function(k) {
     mkinpredict(SFO,
-      c(k_parent_sink = k),
+      c(k_parent = k),
       c(parent = 100),
       sampling_times)
   }
author	Johannes Ranke <jranke@uni-bremen.de>	2020-05-07 22:13:33 +0200
committer	Johannes Ranke <jranke@uni-bremen.de>	2020-05-07 22:14:19 +0200
commit	92bd33824bde6b6b21bfc7e30953092a74d3cce5 (patch)
tree	bb2e08ef15d8a4f4f7b04cf4f5312ec861ec1d1c
parent	67c8163487e776e9a378c9dfcd39c74f6e6bc507 (diff)