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authorJohannes Ranke <jranke@uni-bremen.de>2020-07-07 11:27:44 +0200
committerJohannes Ranke <jranke@uni-bremen.de>2020-07-07 11:27:44 +0200
commit58c6214f459b28b899794f32a60836aef97ac01b (patch)
treebcb8b0f53e27ebb15290f18be8b679262a9e84d1 /R
parente3bc264df69f892e9ad990be22d3ec1b22041daa (diff)
Adapt pfm_degradation to current mkin
use_of_ff = "max" is now the default
Diffstat (limited to 'R')
-rw-r--r--R/pfm_degradation.R31
1 files changed, 7 insertions, 24 deletions
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)
}

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