Adapt pfm_degradation to current mkin

use_of_ff = "max" is now the default

2 files changed, 9 insertions, 26 deletions

diff --git a/DESCRIPTION b/DESCRIPTION
index d125af4..8d0ebeb 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -2,7 +2,7 @@ Package: pfm
 Type: Package
 Title: Utilities for Pesticide Fate Modelling
 Version: 0.5.7
-Date: 2020-04-16
+Date: 2020-06-17
 Authors@R: person("Johannes Ranke", email = "jranke@uni-bremen.de",
                   role = c("aut", "cre", "cph"),
                   comment = c(ORCID = "0000-0003-4371-6538"))
@@ -11,7 +11,7 @@ Description: Utilities for simple calculations of predicted environmental
     pesticide fate modelling software packages.
 Depends:
     R6,
-    mkin
+    mkin (>= 0.9.50.2)
 Imports:
     graphics,
     readr,
diff --git a/R/pfm_degradation.R b/R/pfm_degradation.R
index 6c8610e..832a797 100644
--- a/R/pfm_degradation.R
+++ b/R/pfm_degradation.R
@@ -1,20 +1,3 @@
-# Copyright (C) 2015  Johannes Ranke
-# Contact: jranke@uni-bremen.de
-# This file is part of the R package pfm
-
-# This program is free software: you can redistribute it and/or modify it under
-# the terms of the GNU General Public License as published by the Free Software
-# Foundation, either version 3 of the License, or (at your option) any later
-# version.
-
-# This program is distributed in the hope that it will be useful, but WITHOUT
-# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
-# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
-# details.
-
-# You should have received a copy of the GNU General Public License along with
-# this program. If not, see <http://www.gnu.org/licenses/>
-
 #' Calculate a time course of relative concentrations based on an mkinmod model
 #'
 #' @import mkin
@@ -30,9 +13,10 @@
 #' @author Johannes Ranke
 #' @examples
 #' head(pfm_degradation("SFO", DT50 = 10))
-pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink = log(2)/DT50),
-                            years = 1, step_days = 1,
-                            times = seq(0, years * 365, by = step_days))
+pfm_degradation <- function(model = "SFO",
+  DT50 = 1000, parms = c(k_parent = log(2)/DT50),
+  years = 1, step_days = 1,
+  times = seq(0, years * 365, by = step_days))
 {
   if (model %in% c("SFO", "FOMC", "DFOP", "HS", "IORE")) {
     model <- mkinmod(parent = list(type = model))
@@ -40,9 +24,8 @@ pfm_degradation <- function(model = "SFO", DT50 = 1000, parms = c(k_parent_sink
   initial_state = c(1, rep(0, length(model$diffs) - 1))
   names(initial_state) <- names(model$diffs)
   time_course <- mkinpredict(model, odeparms = parms, 
-                             odeini = initial_state,
-                             outtimes = times,
-                             solution_type = ifelse(length(model$spec) == 1,
-                                                    "analytical", "deSolve"))
+    odeini = initial_state,
+    outtimes = times,
+    solution_type = ifelse(length(model$spec) == 1, "analytical", "deSolve"))
   invisible(time_course)
 }