From 081b5f25cc4ef779175307d9ce20672e0573b7c9 Mon Sep 17 00:00:00 2001 From: jranke Date: Tue, 24 Apr 2012 17:33:56 +0000 Subject: - Added the reference fit data for FOCUS 2006 datasets from the kinfit package - Used these data in unit tests for parent only models - Fixed SFORB data and calculation of formation fractions along the way - Reintroduced the test for the Schaefer 2007 data - Got rid of the mkinmod unit tests - they are too hard to maintain and the mkinfit tests test the model definitions as well git-svn-id: svn+ssh://svn.r-forge.r-project.org/svnroot/kinfit/pkg/mkin@32 edb9625f-4e0d-4859-8d74-9fd3b1da38cb --- man/FOCUS_2006_DFOP_ref_A_to_B.Rd | 39 +++++++++++++++++++++++++++++++++++++++ man/FOCUS_2006_FOMC_ref_A_to_F.Rd | 38 ++++++++++++++++++++++++++++++++++++++ man/FOCUS_2006_HS_ref_A_to_F.Rd | 39 +++++++++++++++++++++++++++++++++++++++ man/FOCUS_2006_SFO_ref_A_to_F.Rd | 37 +++++++++++++++++++++++++++++++++++++ man/mkinfit.Rd | 8 ++++++-- 5 files changed, 159 insertions(+), 2 deletions(-) create mode 100644 man/FOCUS_2006_DFOP_ref_A_to_B.Rd create mode 100644 man/FOCUS_2006_FOMC_ref_A_to_F.Rd create mode 100644 man/FOCUS_2006_HS_ref_A_to_F.Rd create mode 100644 man/FOCUS_2006_SFO_ref_A_to_F.Rd (limited to 'man') diff --git a/man/FOCUS_2006_DFOP_ref_A_to_B.Rd b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd new file mode 100644 index 0000000..88bd4ac --- /dev/null +++ b/man/FOCUS_2006_DFOP_ref_A_to_B.Rd @@ -0,0 +1,39 @@ +\name{FOCUS_2006_DFOP_ref_A_to_B} +\Rdversion{1.1} +\alias{FOCUS_2006_DFOP_ref_A_to_B} +\docType{data} +\title{ +Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_DFOP_ref_A_to_B)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{f}}{The fitted f parameter} + \item{\code{k1}}{The fitted k1 parameter} + \item{\code{k2}}{The fitted k2 parameter} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration} Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + \url{http://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_DFOP_ref_A_to_B) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_FOMC_ref_A_to_F.Rd b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd new file mode 100644 index 0000000..2fcc2db --- /dev/null +++ b/man/FOCUS_2006_FOMC_ref_A_to_F.Rd @@ -0,0 +1,38 @@ +\name{FOCUS_2006_FOMC_ref_A_to_F} +\Rdversion{1.1} +\alias{FOCUS_2006_FOMC_ref_A_to_F} +\docType{data} +\title{ +Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_FOMC_ref_A_to_F)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{alpha}}{The fitted alpha parameter} + \item{\code{beta}}{The fitted beta parameter} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration} Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + \url{http://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_FOMC_ref_A_to_F) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_HS_ref_A_to_F.Rd b/man/FOCUS_2006_HS_ref_A_to_F.Rd new file mode 100644 index 0000000..6fc9993 --- /dev/null +++ b/man/FOCUS_2006_HS_ref_A_to_F.Rd @@ -0,0 +1,39 @@ +\name{FOCUS_2006_HS_ref_A_to_F} +\Rdversion{1.1} +\alias{FOCUS_2006_HS_ref_A_to_F} +\docType{data} +\title{ +Results of fitting the HS model to Datasets A to F of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_HS_ref_A_to_F)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{tb}}{The fitted tb parameter} + \item{\code{k1}}{The fitted k1 parameter} + \item{\code{k2}}{The fitted k2 parameter} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration} Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + \url{http://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_HS_ref_A_to_F) +} +\keyword{datasets} diff --git a/man/FOCUS_2006_SFO_ref_A_to_F.Rd b/man/FOCUS_2006_SFO_ref_A_to_F.Rd new file mode 100644 index 0000000..19650ed --- /dev/null +++ b/man/FOCUS_2006_SFO_ref_A_to_F.Rd @@ -0,0 +1,37 @@ +\name{FOCUS_2006_SFO_ref_A_to_F} +\Rdversion{1.1} +\alias{FOCUS_2006_SFO_ref_A_to_F} +\docType{data} +\title{ +Results of fitting the SFO model to Datasets A to F of FOCUS (2006) +} +\description{ +A table with the fitted parameters and the resulting DT50 and DT90 values +generated with different software packages. Taken directly from FOCUS (2006). +The results from fitting the data with the Topfit software was removed, as +the initial concentration of the parent compound was fixed to a value of 100 +in this fit. +} +\usage{data(FOCUS_2006_SFO_ref_A_to_F)} +\format{ + A data frame containing the following variables. + \describe{ + \item{\code{package}}{a factor giving the name of the software package} + \item{\code{M0}}{The fitted initial concentration of the parent compound} + \item{\code{k}}{The fitted first-order degradation rate constant} + \item{\code{DT50}}{The resulting half-life of the parent compound} + \item{\code{DT90}}{The resulting DT90 of the parent compound} + \item{\code{dataset}}{The FOCUS dataset that was used} + } +} +\source{ + FOCUS (2006) \dQuote{Guidance Document on Estimating Persistence and + Degradation Kinetics from Environmental Fate Studies on Pesticides in EU + Registration} Report of the FOCUS Work Group on Degradation Kinetics, + EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, + \url{http://focus.jrc.ec.europa.eu/dk} +} +\examples{ +data(FOCUS_2006_SFO_ref_A_to_F) +} +\keyword{datasets} diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index 0c8e48f..5f70dae 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -17,7 +17,8 @@ mkinfit(mkinmod, observed, solution_type = "auto", plot = FALSE, quiet = FALSE, err = NULL, weight = "none", scaleVar = FALSE, - atol = 1e-6, n.outtimes, ...) + atol = 1e-6, n.outtimes, + trace_parms, ...) } \arguments{ \item{mkinmod}{ @@ -92,6 +93,9 @@ mkinfit(mkinmod, observed, the numerical solver if that is used (see \code{solution} argument. The default value is 100. } + \item{trace_parms}{ + Should a trace of the parameter values be listed? + } \item{\dots}{ Further arguments that will be passed to \code{\link{modFit}}. } @@ -101,7 +105,7 @@ mkinfit(mkinmod, observed, A summary can be obtained by \code{\link{summary.mkinfit}}. } \author{ - Johannes Ranke + Johannes Ranke } \examples{ # One parent compound, one metabolite, both single first order. -- cgit v1.2.1