From 59e2c3b5ce470ace53b93ad5e6e7d9acbfe86f21 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 25 Apr 2014 18:43:51 +0200 Subject: McCall 2,4,5-T dataset, lower bound for transform_rates=FALSE --- DESCRIPTION | 2 +- NAMESPACE | 3 ++- R/mkinfit.R | 13 ++++++++++-- R/transform_odeparms.R | 4 ++-- data/mccall81_245T_soil_metabolism.RData | Bin 0 -> 786 bytes man/mccall81_245T_soil_metabolism.Rd | 35 +++++++++++++++++++++++++++++++ man/mkinfit.Rd | 1 + 7 files changed, 52 insertions(+), 6 deletions(-) create mode 100644 data/mccall81_245T_soil_metabolism.RData create mode 100644 man/mccall81_245T_soil_metabolism.Rd 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 diff --git a/NAMESPACE b/NAMESPACE index 4128213..dfa9e9b 100644 --- a/NAMESPACE +++ b/NAMESPACE @@ -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 new file mode 100644 index 0000000..1e6efa7 Binary files /dev/null and b/data/mccall81_245T_soil_metabolism.RData differ 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 -- cgit v1.2.1