diff options
| -rw-r--r-- | DESCRIPTION | 2 | ||||
| -rw-r--r-- | NAMESPACE | 3 | ||||
| -rw-r--r-- | R/mkinfit.R | 13 | ||||
| -rw-r--r-- | R/transform_odeparms.R | 4 | ||||
| -rw-r--r-- | data/mccall81_245T_soil_metabolism.RData | bin | 0 -> 786 bytes | |||
| -rw-r--r-- | man/mccall81_245T_soil_metabolism.Rd | 35 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 1 |
7 files changed, 52 insertions, 6 deletions
diff --git a/DESCRIPTION b/DESCRIPTION index f348248..345438e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -17,7 +17,7 @@ Description: Calculation routines based on the FOCUS Kinetics Report (2006). implied for correctness of results or fitness for a particular purpose. An experimental graphical user interface is included which is based on the gWidgetsWWW2 package on GitHub (http://github.com/jverzani/gWidgetsWWW2/) -Depends: minpack.lm +Depends: minpack.lm, rootSolve Imports: FME, deSolve Suggests: knitr, RUnit, gWidgetsWWW2, RSVGTipsDevice License: GPL @@ -5,5 +5,6 @@ exportPattern(".") import( FME, deSolve, - minpack.lm + minpack.lm, + rootSolve ) diff --git a/R/mkinfit.R b/R/mkinfit.R index a623146..16b4ff3 100644 --- a/R/mkinfit.R +++ b/R/mkinfit.R @@ -208,8 +208,17 @@ mkinfit <- function(mkinmod, observed, return(mC)
}
+ lower <- rep(-Inf, length(c(state.ini.optim, parms.optim)))
+ names(lower) <- c(names(state.ini.optim), names(parms.optim))
+ if (!transform_rates) {
+ index_k <- grep("^k_", names(lower))
+ lower[index_k] <- 0
+ other_rate_parms <- intersect(c("alpha", "beta", "k1", "k2"), names(lower))
+ lower[other_rate_parms] <- 0
+ }
+
fit <- modFit(cost, c(state.ini.optim, parms.optim),
- method = method.modFit, control = control.modFit, ...)
+ method = method.modFit, control = control.modFit, lower = lower, ...)
# Reiterate the fit until convergence of the variance components (IRLS)
# if requested by the user
@@ -234,7 +243,7 @@ mkinfit <- function(mkinmod, observed, sigma.old <- sqrt(fit$var_ms_unweighted)
observed[err] <- sqrt(fit$var_ms_unweighted)[as.character(observed$name)]
fit <- modFit(cost, fit$par, method = method.modFit,
- control = control.modFit, ...)
+ control = control.modFit, lower = lower, ...)
reweight.diff = sum((sqrt(fit$var_ms_unweighted) - sigma.old)^2)
if (!quiet) {
cat("Iteration", n.iter, "yields variance estimates:\n")
diff --git a/R/transform_odeparms.R b/R/transform_odeparms.R index 31200c7..24de074 100644 --- a/R/transform_odeparms.R +++ b/R/transform_odeparms.R @@ -44,8 +44,8 @@ transform_odeparms <- function(parms, mod_vars, }
}
- # Transform parameters also for FOMC, DFOP and HS models if requested
- for (pname in c("alpha", "beta", "k1", "k2", "tb")) {
+ # Transform rate and fraction parameters also for FOMC, DFOP and HS models if requested
+ for (pname in c("alpha", "beta", "k1", "k2")) {
if (!is.na(parms[pname])) {
transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])
transparms[pname] <- ifelse(transform_rates, log(parms[pname]), parms[pname])
diff --git a/data/mccall81_245T_soil_metabolism.RData b/data/mccall81_245T_soil_metabolism.RData Binary files differnew file mode 100644 index 0000000..1e6efa7 --- /dev/null +++ b/data/mccall81_245T_soil_metabolism.RData diff --git a/man/mccall81_245T_soil_metabolism.Rd b/man/mccall81_245T_soil_metabolism.Rd new file mode 100644 index 0000000..2ccc23d --- /dev/null +++ b/man/mccall81_245T_soil_metabolism.Rd @@ -0,0 +1,35 @@ +\name{mccall81_245T_soil_metabolism}
+\Rdversion{1.1}
+\alias{commerce}
+\alias{catlin}
+\alias{fargo}
+\alias{keith}
+\alias{walla_walla}
+\alias{cecil}
+\docType{data}
+\title{
+ Datasets on aerobic soil metabolism of 2,4,5-T in six soils
+}
+\description{
+ Time course of 2,4,5-trichlorophenoxyacetic acid, and the corresponding 2,4,5-trichlorophenol and
+ 2,4,5-trichloroanisole as recovered in diethylether extracts.
+}
+\usage{mccall81_245T_soil_metabolism}
+\format{
+ 6 dataframes containing the following variables.
+ \describe{
+ \item{\code{name}}{the name of the compound observed. Note that T245 is used as an acronym for 2,4,5-T. T245 is
+ a legitimate object name in R, which is necessary for
+ specifying models using \code{\link{mkinmod}}.}
+ \item{\code{time}}{a numeric vector containing sampling times in days after treatment}
+ \item{\code{value}}{a numeric vector containing concentrations in percent of applied radioactivity}
+ }
+}
+\source{
+ McCall P, Vrona SA, Kelley SS (1981) Fate of uniformly carbon-14 ring labeled 2,4,5-Trichlorophenoxyacetic acid and 2,4-dichlorophenoxyacetic acid. J Agric Chem 29, 100-107
+ \url{http://dx.doi.org/10.1021/jf00103a026}
+}
+\examples{
+ commerce
+}
+\keyword{datasets}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 839580a..823ceee 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -110,6 +110,7 @@ mkinfit(mkinmod, observed, assumption of normal distribution of the estimator. If TRUE, also alpha and beta parameters of the FOMC model are log-transformed, as well as k1 and k2 rate constants for the DFOP and HS models. + If TRUE, zero is used as a lower bound for the rates in the optimisation. } \item{transform_fractions}{ Boolean specifying if formation fractions constants should be transformed in the |