From 39d5dc6988389f026d5165cac208ec63d0645a77 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Fri, 22 Feb 2019 09:46:39 +0100
Subject: Further adaptations for the logistic model

- Make mmkin compatible
- Return DT50 values corresponding to k0 and kmax
- Turn incompatible parameter names in parms.ini from an error to a
warning, in order to make it possible to use this argument in calls to
mmkin
---
 R/endpoints.R            | 5 +++++
 R/mkinfit.R              | 4 ++--
 R/mmkin.R                | 4 ++--
 man/logistic.solution.Rd | 7 ++++---
 4 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/R/endpoints.R b/R/endpoints.R
index 80450185..f8a44c4d 100644
--- a/R/endpoints.R
+++ b/R/endpoints.R
@@ -166,6 +166,11 @@ endpoints <- function(fit) {
       r = parms.all["r"]
       DT50 = (1/r) * log(1 - ((kmax/k0) * (1 - 2^(r/kmax))))
       DT90 = (1/r) * log(1 - ((kmax/k0) * (1 - 10^(r/kmax))))
+
+      DT50_k0 = log(2)/k0
+      DT50_kmax = log(2)/kmax
+      ep$distimes[obs_var, c("DT50_k0")] = DT50_k0
+      ep$distimes[obs_var, c("DT50_kmax")] = DT50_kmax
     }
     ep$distimes[obs_var, c("DT50", "DT90")] = c(DT50, DT90)
   }
diff --git a/R/mkinfit.R b/R/mkinfit.R
index 40413125..2dec3a72 100644
--- a/R/mkinfit.R
+++ b/R/mkinfit.R
@@ -99,10 +99,10 @@ mkinfit <- function(mkinmod, observed,
   # Define starting values for parameters where not specified by the user
   if (parms.ini[[1]] == "auto") parms.ini = vector()
 
-  # Prevent inital parameter specifications that are not in the model
+  # Warn for inital parameter specifications that are not in the model
   wrongpar.names <- setdiff(names(parms.ini), mkinmod$parms)
   if (length(wrongpar.names) > 0) {
-    stop("Initial parameter(s) ", paste(wrongpar.names, collapse = ", "),
+    warning("Initial parameter(s) ", paste(wrongpar.names, collapse = ", "),
          " not used in the model")
   }
 
diff --git a/R/mmkin.R b/R/mmkin.R
index 63542f4f..b713ae74 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -1,4 +1,4 @@
-# Copyright (C) 2015 Johannes Ranke
+# Copyright (C) 2015,2019 Johannes Ranke
 # Contact: jranke@uni-bremen.de
 # The summary function is an adapted and extended version of summary.modFit
 # from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn
@@ -22,7 +22,7 @@
 mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets,
                   cores = round(detectCores()/2), cluster = NULL, ...)
 {
-  parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE")
+  parent_models_available = c("SFO", "FOMC", "DFOP", "HS", "SFORB", "IORE", "logistic")
   n.m <- length(models)
   n.d <- length(datasets)
   n.fits <- n.m * n.d
diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd
index 67e60983..05b6c0aa 100644
--- a/man/logistic.solution.Rd
+++ b/man/logistic.solution.Rd
@@ -2,7 +2,7 @@
 \alias{logistic.solution}
 \title{ Logistic kinetics }
 \description{
-  Function describing exponential decline from a defined starting value, with 
+  Function describing exponential decline from a defined starting value, with
   an increasing rate constant, supposedly caused by microbial growth
 }
 \usage{
@@ -28,11 +28,11 @@ logistic.solution(t, parent.0, kmax, k0, r)
   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} 
+  \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), 
+  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),
@@ -63,5 +63,6 @@ logistic.solution(t, parent.0, kmax, k0, r)
   m <- mkinfit("logistic", d_2_1, quiet = TRUE)
   plot_sep(m)
   summary(m)$bpar
+  endpoints(m)$distimes
 }
 \keyword{ manip }
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