diff options
| -rw-r--r-- | R/endpoints.R | 5 | ||||
| -rw-r--r-- | R/mkinfit.R | 4 | ||||
| -rw-r--r-- | R/mmkin.R | 4 | ||||
| -rw-r--r-- | 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")
}
@@ -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 } |