From 9ac853c7ceece333099021974025d07e75be2b33 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 12 May 2020 08:07:07 +0200 Subject: Documentation improvements, rebuild static docs --- man/AIC.mmkin.Rd | 2 +- man/DFOP.solution.Rd | 16 +++---- man/FOMC.solution.Rd | 26 +++++----- man/HS.solution.Rd | 16 +++---- man/IORE.solution.Rd | 8 ++-- man/SFO.solution.Rd | 16 +++---- man/SFORB.solution.Rd | 18 +++---- man/add_err.Rd | 2 +- man/confint.mkinfit.Rd | 14 +++--- man/endpoints.Rd | 6 +-- man/get_deg_func.Rd | 2 +- man/ilr.Rd | 8 ++-- man/logLik.mkinfit.Rd | 6 +-- man/logistic.solution.Rd | 18 +++---- man/max_twa_parent.Rd | 12 ++--- man/mkinerrplot.Rd | 4 +- man/mkinfit.Rd | 118 ++++++++++++++++++++++++---------------------- man/mkinmod.Rd | 59 ++++++++++++----------- man/mkinparplot.Rd | 2 +- man/mkinresplot.Rd | 6 +-- man/mmkin.Rd | 6 +-- man/nafta.Rd | 22 ++++----- man/nlme.Rd | 6 +-- man/nlme.mmkin.Rd | 2 +- man/plot.mkinfit.Rd | 2 +- man/plot.mmkin.Rd | 2 +- man/plot.nlme.mmkin.Rd | 2 +- man/sigma_twocomp.Rd | 8 ++-- man/summary.mkinfit.Rd | 50 ++++++++++---------- man/transform_odeparms.Rd | 2 +- 30 files changed, 236 insertions(+), 225 deletions(-) (limited to 'man') diff --git a/man/AIC.mmkin.Rd b/man/AIC.mmkin.Rd index a10d0aeb..13081561 100644 --- a/man/AIC.mmkin.Rd +++ b/man/AIC.mmkin.Rd @@ -19,7 +19,7 @@ column.} } \value{ As in the generic method (a numeric value for single fits, or a - dataframe if there are several fits in the column). +dataframe if there are several fits in the column). } \description{ Provides a convenient way to compare different kinetic models fitted to the diff --git a/man/DFOP.solution.Rd b/man/DFOP.solution.Rd index 8ada60c5..d8c4553e 100644 --- a/man/DFOP.solution.Rd +++ b/man/DFOP.solution.Rd @@ -32,15 +32,15 @@ two exponential decline functions. } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and 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} +and 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} } \seealso{ Other parent solutions: diff --git a/man/FOMC.solution.Rd b/man/FOMC.solution.Rd index e5e46c87..eeee85f9 100644 --- a/man/FOMC.solution.Rd +++ b/man/FOMC.solution.Rd @@ -30,8 +30,8 @@ in the original equation. } \note{ The solution of the FOMC kinetic model reduces to the - \code{\link{SFO.solution}} for large values of \code{alpha} and - \code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. +\code{\link{SFO.solution}} for large values of \code{alpha} and +\code{beta} with \eqn{k = \frac{\beta}{\alpha}}{k = beta/alpha}. } \examples{ @@ -40,20 +40,20 @@ The solution of the FOMC kinetic model reduces to the } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and 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} +and 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} - Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: - A new model based on spatial variability. \emph{Environmental Science and - Technology} \bold{24}, 1032-1038 +Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: +A new model based on spatial variability. \emph{Environmental Science and +Technology} \bold{24}, 1032-1038 } \seealso{ Other parent solutions: diff --git a/man/HS.solution.Rd b/man/HS.solution.Rd index f72df23b..2940e949 100644 --- a/man/HS.solution.Rd +++ b/man/HS.solution.Rd @@ -33,15 +33,15 @@ between them. } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and 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} +and 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} } \seealso{ Other parent solutions: diff --git a/man/IORE.solution.Rd b/man/IORE.solution.Rd index e1f1be1a..1150f023 100644 --- a/man/IORE.solution.Rd +++ b/man/IORE.solution.Rd @@ -25,9 +25,9 @@ a concentration dependent rate constant. } \note{ The solution of the IORE kinetic model reduces to the - \code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can - be transformed to equivalent parameters of the FOMC mode - see the NAFTA - guidance for details. +\code{\link{SFO.solution}} if N = 1. The parameters of the IORE model can +be transformed to equivalent parameters of the FOMC mode - see the NAFTA +guidance for details. } \examples{ @@ -46,7 +46,7 @@ The solution of the IORE kinetic model reduces to the } \references{ NAFTA Technical Working Group on Pesticides (not dated) Guidance - for Evaluating and Calculating Degradation Kinetics in Environmental Media +for Evaluating and Calculating Degradation Kinetics in Environmental Media } \seealso{ Other parent solutions: diff --git a/man/SFO.solution.Rd b/man/SFO.solution.Rd index 6892cccc..c0aac237 100644 --- a/man/SFO.solution.Rd +++ b/man/SFO.solution.Rd @@ -26,15 +26,15 @@ Function describing exponential decline from a defined starting value. } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and 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} +and 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} } \seealso{ Other parent solutions: diff --git a/man/SFORB.solution.Rd b/man/SFORB.solution.Rd index 98a8c684..dc78d1f1 100644 --- a/man/SFORB.solution.Rd +++ b/man/SFORB.solution.Rd @@ -20,7 +20,7 @@ fraction.} } \value{ The value of the response variable, which is the sum of free and - bound fractions at time \code{t}. +bound fractions at time \code{t}. } \description{ Function describing the solution of the differential equations describing @@ -36,15 +36,15 @@ and no substance in the bound fraction. } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and 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} +and 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} } \seealso{ Other parent solutions: diff --git a/man/add_err.Rd b/man/add_err.Rd index 3452923e..1171e0fd 100644 --- a/man/add_err.Rd +++ b/man/add_err.Rd @@ -40,7 +40,7 @@ seed is not set.} } \value{ A list of datasets compatible with \code{\link{mmkin}}, i.e. the - components of the list are datasets compatible with \code{\link{mkinfit}}. +components of the list are datasets compatible with \code{\link{mkinfit}}. } \description{ Normally distributed errors are added to data predicted for a specific diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd index 81d7a6e8..f295afc4 100644 --- a/man/confint.mkinfit.Rd +++ b/man/confint.mkinfit.Rd @@ -45,7 +45,7 @@ applied to the likelihood based on the transformed parameters?} transformed parameters, should we backtransform the parameters with their confidence intervals?} -\item{cores}{The number of cores to be used for multicore processing. +\item{cores}{The number of cores to be used for multicore processing. On Windows machines, cores > 1 is currently not supported.} \item{quiet}{Should we suppress the message "Profiling the likelihood"} @@ -54,7 +54,7 @@ On Windows machines, cores > 1 is currently not supported.} } \value{ A matrix with columns giving lower and upper confidence limits for - each parameter. +each parameter. } \description{ The default method 'quadratic' is based on the quadratic approximation of @@ -143,10 +143,10 @@ confint(f_tc_2, "parent_0", method = "quadratic") \references{ Bates DM and Watts GW (1988) Nonlinear regression analysis & its applications - Pawitan Y (2013) In all likelihood - Statistical modelling and - inference using likelihood. Clarendon Press, Oxford. +Pawitan Y (2013) In all likelihood - Statistical modelling and +inference using likelihood. Clarendon Press, Oxford. - Venzon DJ and Moolgavkar SH (1988) A Method for Computing - Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, - 87–94. +Venzon DJ and Moolgavkar SH (1988) A Method for Computing +Profile-Likelihood Based Confidence Intervals, Applied Statistics, 37, +87–94. } diff --git a/man/endpoints.Rd b/man/endpoints.Rd index 26b5ee08..49f44d74 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -13,9 +13,9 @@ endpoints(fit) } \value{ A list with a matrix of dissipation times named distimes, - and, if applicable, a vector of formation fractions named ff - and, if the SFORB model was in use, a vector of eigenvalues - of these SFORB models, equivalent to DFOP rate constants +and, if applicable, a vector of formation fractions named ff +and, if the SFORB model was in use, a vector of eigenvalues +of these SFORB models, equivalent to DFOP rate constants } \description{ This function calculates DT50 and DT90 values as well as formation fractions diff --git a/man/get_deg_func.Rd b/man/get_deg_func.Rd index 1d8a3de9..75743448 100644 --- a/man/get_deg_func.Rd +++ b/man/get_deg_func.Rd @@ -8,7 +8,7 @@ get_deg_func() } \value{ A function that was likely previously assigned from within - nlme.mmkin +nlme.mmkin } \description{ Retrieve a degradation function from the mmkin namespace diff --git a/man/ilr.Rd b/man/ilr.Rd index 0cbd7e2c..f691ec23 100644 --- a/man/ilr.Rd +++ b/man/ilr.Rd @@ -15,8 +15,8 @@ sensible for vectors with all elements being greater than zero.} } \value{ The result of the forward or backward transformation. The returned - components always sum to 1 for the case of the inverse log-ratio - transformation. +components always sum to 1 for the case of the inverse log-ratio +transformation. } \description{ This implementation is a special case of the class of isometric log-ratio @@ -48,11 +48,11 @@ ilr(c(b[1:3], 1 - sum(b[1:3]))) # Gives c(0.1, 0.3, 0.5) } \references{ Peter Filzmoser, Karel Hron (2008) Outlier Detection for - Compositional Data Using Robust Methods. Math Geosci 40 233-248 +Compositional Data Using Robust Methods. Math Geosci 40 233-248 } \seealso{ Another implementation can be found in R package - \code{robCompositions}. +\code{robCompositions}. } \author{ René Lehmann and Johannes Ranke diff --git a/man/logLik.mkinfit.Rd b/man/logLik.mkinfit.Rd index 502fb4d7..637570e4 100644 --- a/man/logLik.mkinfit.Rd +++ b/man/logLik.mkinfit.Rd @@ -13,8 +13,8 @@ } \value{ An object of class \code{\link{logLik}} with the number of estimated - parameters (degradation model parameters plus variance model parameters) - as attribute. +parameters (degradation model parameters plus variance model parameters) +as attribute. } \description{ This function returns the product of the likelihood densities of each @@ -45,7 +45,7 @@ and the fitted error model parameters. } \seealso{ Compare the AIC of columns of \code{\link{mmkin}} objects using - \code{\link{AIC.mmkin}}. +\code{\link{AIC.mmkin}}. } \author{ Johannes Ranke diff --git a/man/logistic.solution.Rd b/man/logistic.solution.Rd index 33b3d44a..efa12e7a 100644 --- a/man/logistic.solution.Rd +++ b/man/logistic.solution.Rd @@ -26,7 +26,7 @@ an increasing rate constant, supposedly caused by microbial growth } \note{ The solution of the logistic model reduces to the - \code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}. +\code{\link{SFO.solution}} if \code{k0} is equal to \code{kmax}. } \examples{ @@ -67,15 +67,15 @@ The solution of the logistic model reduces to the } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} FOCUS (2014) \dQuote{Generic guidance for Estimating Persistence - and 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} +and 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} } \seealso{ Other parent solutions: diff --git a/man/max_twa_parent.Rd b/man/max_twa_parent.Rd index 7c9f4861..107eebd0 100644 --- a/man/max_twa_parent.Rd +++ b/man/max_twa_parent.Rd @@ -48,8 +48,8 @@ factor (f_twa) is calculated.} } \value{ For \code{max_twa_parent}, a numeric vector, named using the - \code{windows} argument. For the other functions, a numeric vector of - length one (also known as 'a number'). +\code{windows} argument. For the other functions, a numeric vector of +length one (also known as 'a number'). } \description{ This function calculates maximum moving window time weighted average @@ -66,10 +66,10 @@ soil section of the FOCUS guidance. } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \author{ Johannes Ranke diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd index 9564ec19..82178aa9 100644 --- a/man/mkinerrplot.Rd +++ b/man/mkinerrplot.Rd @@ -50,7 +50,7 @@ be passed on to \code{\link{legend}}.} } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the squared residuals for the specified subset of the @@ -70,7 +70,7 @@ mkinerrplot(fit) } \seealso{ \code{\link{mkinplot}}, for a way to plot the data and the fitted - lines of the mkinfit object. +lines of the mkinfit object. } \author{ Johannes Ranke diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index db3f5f3e..97dffef7 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -3,10 +3,6 @@ \name{mkinfit} \alias{mkinfit} \title{Fit a kinetic model to data with one or more state variables} -\source{ -Rocke, David M. und Lorenzato, Stefan (1995) A two-component model - for measurement error in analytical chemistry. Technometrics 37(2), 176-184. -} \usage{ mkinfit( mkinmod, @@ -53,16 +49,16 @@ not observed in degradation data, because there is a lower limit of detection.} \item{parms.ini}{A named vector of initial values for the parameters, - including parameters to be optimised and potentially also fixed parameters - as indicated by \code{fixed_parms}. If set to "auto", initial values for - rate constants are set to default values. Using parameter names that are - not in the model gives an error. +including parameters to be optimised and potentially also fixed parameters +as indicated by \code{fixed_parms}. If set to "auto", initial values for +rate constants are set to default values. Using parameter names that are +not in the model gives an error. - It is possible to only specify a subset of the parameters that the model - needs. You can use the parameter lists "bparms.ode" from a previously - fitted model, which contains the differential equation parameters from - this model. This works nicely if the models are nested. An example is - given below.} +It is possible to only specify a subset of the parameters that the model +needs. You can use the parameter lists "bparms.ode" from a previously +fitted model, which contains the differential equation parameters from +this model. This works nicely if the models are nested. An example is +given below.} \item{state.ini}{A named vector of initial values for the state variables of the model. In case the observed variables are represented by more than one @@ -141,48 +137,50 @@ is 1e-8, lower than in \code{\link{lsoda}}.} is 1e-10, much lower than in \code{\link{lsoda}}.} \item{error_model}{If the error model is "const", a constant standard - deviation is assumed. +deviation is assumed. - If the error model is "obs", each observed variable is assumed to have its - own variance. +If the error model is "obs", each observed variable is assumed to have its +own variance. - If the error model is "tc" (two-component error model), a two component - error model similar to the one described by Rocke and Lorenzato (1995) is - used for setting up the likelihood function. Note that this model - deviates from the model by Rocke and Lorenzato, as their model implies - that the errors follow a lognormal distribution for large values, not a - normal distribution as assumed by this method.} +If the error model is "tc" (two-component error model), a two component +error model similar to the one described by Rocke and Lorenzato (1995) is +used for setting up the likelihood function. Note that this model +deviates from the model by Rocke and Lorenzato, as their model implies +that the errors follow a lognormal distribution for large values, not a +normal distribution as assumed by this method.} \item{error_model_algorithm}{If "auto", the selected algorithm depends on - the error model. If the error model is "const", unweighted nonlinear - least squares fitting ("OLS") is selected. If the error model is "obs", or - "tc", the "d_3" algorithm is selected. - - The algorithm "d_3" will directly minimize the negative log-likelihood and - - independently - also use the three step algorithm described below. The - fit with the higher likelihood is returned. +the error model. If the error model is "const", unweighted nonlinear +least squares fitting ("OLS") is selected. If the error model is "obs", or +"tc", the "d_3" algorithm is selected. + +The algorithm "d_3" will directly minimize the negative log-likelihood and +\itemize{ +\item independently - also use the three step algorithm described below. The +fit with the higher likelihood is returned. +} - The algorithm "direct" will directly minimize the negative log-likelihood. +The algorithm "direct" will directly minimize the negative log-likelihood. - The algorithm "twostep" will minimize the negative log-likelihood after an - initial unweighted least squares optimisation step. +The algorithm "twostep" will minimize the negative log-likelihood after an +initial unweighted least squares optimisation step. - The algorithm "threestep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, and then minimizes the negative log-likelihood with free - degradation and error model parameters. +The algorithm "threestep" starts with unweighted least squares, then +optimizes only the error model using the degradation model parameters +found, and then minimizes the negative log-likelihood with free +degradation and error model parameters. - The algorithm "fourstep" starts with unweighted least squares, then - optimizes only the error model using the degradation model parameters - found, then optimizes the degradation model again with fixed error model - parameters, and finally minimizes the negative log-likelihood with free - degradation and error model parameters. +The algorithm "fourstep" starts with unweighted least squares, then +optimizes only the error model using the degradation model parameters +found, then optimizes the degradation model again with fixed error model +parameters, and finally minimizes the negative log-likelihood with free +degradation and error model parameters. - The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with - unweighted least squares, and then iterates optimization of the error - model parameters and subsequent optimization of the degradation model - using those error model parameters, until the error model parameters - converge.} +The algorithm "IRLS" (Iteratively Reweighted Least Squares) starts with +unweighted least squares, and then iterates optimization of the error +model parameters and subsequent optimization of the degradation model +using those error model parameters, until the error model parameters +converge.} \item{reweight.tol}{Tolerance for the convergence criterion calculated from the error model parameters in IRLS fits.} @@ -196,7 +194,7 @@ the error model parameters in IRLS fits.} } \value{ A list with "mkinfit" in the class attribute. A summary can be - obtained by \code{\link{summary.mkinfit}}. +obtained by \code{\link{summary.mkinfit}}. } \description{ This function maximises the likelihood of the observed data using the Port @@ -214,9 +212,9 @@ estimators. } \note{ When using the "IORE" submodel for metabolites, fitting with - "transform_rates = TRUE" (the default) often leads to failures of the - numerical ODE solver. In this situation it may help to switch off the - internal rate transformation. +"transform_rates = TRUE" (the default) often leads to failures of the +numerical ODE solver. In this situation it may help to switch off the +internal rate transformation. } \examples{ @@ -268,7 +266,7 @@ fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.o } \dontrun{ -# Weighted fits, including IRLS +# Weighted fits, including IRLS (error_model = "obs") SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max") f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) @@ -280,16 +278,24 @@ summary(f.tc) } +} +\references{ +Rocke DM and Lorenzato S (1995) A two-component model +for measurement error in analytical chemistry. \emph{Technometrics} 37(2), 176-184. + +Ranke J and Meinecke S (2019) Error Models for the Kinetic Evaluation of Chemical +Degradation Data. \emph{Environments} 6(12) 124 +\href{https://doi.org/10.3390/environments6120124}{doi:10.3390/environments6120124}. } \seealso{ Plotting methods \code{\link{plot.mkinfit}} and - \code{\link{mkinparplot}}. +\code{\link{mkinparplot}}. - Comparisons of models fitted to the same data can be made using - \code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}. +Comparisons of models fitted to the same data can be made using +\code{\link{AIC}} by virtue of the method \code{\link{logLik.mkinfit}}. - Fitting of several models to several datasets in a single call to - \code{\link{mmkin}}. +Fitting of several models to several datasets in a single call to +\code{\link{mmkin}}. } \author{ Johannes Ranke diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd index a5736be7..6a6d2027 100644 --- a/man/mkinmod.Rd +++ b/man/mkinmod.Rd @@ -44,25 +44,30 @@ applicable to give detailed information about the C function being built.} } \value{ A list of class \code{mkinmod} for use with \code{\link{mkinfit}}, - containing, among others, - \item{diffs}{ - A vector of string representations of differential equations, one for - each modelling variable. - } - \item{map}{ - A list containing named character vectors for each observed variable, - specifying the modelling variables by which it is represented. - } - \item{use_of_ff}{ - The content of \code{use_of_ff} is passed on in this list component. - } - \item{coefmat}{ - The coefficient matrix, if the system of differential equations can be - represented by one. - } - \item{cf}{ - If generated, the compiled function as returned by cfunction. - } +containing, among others, +\item{diffs}{ +A vector of string representations of differential equations, one for +each modelling variable. +} +\item{map}{ +A list containing named character vectors for each observed variable, +specifying the modelling variables by which it is represented. +} +\item{use_of_ff}{ +The content of \code{use_of_ff} is passed on in this list component. +} +\item{deg_func}{ +If generated, a function containing the solution of the degradation +model. +} +\item{coefmat}{ +The coefficient matrix, if the system of differential equations can be +represented by one. +} +\item{cf}{ +If generated, a compiled function calculating the derivatives as +returned by cfunction. +} } \description{ The function usually takes several expressions, each assigning a compound @@ -76,8 +81,8 @@ in the FOCUS and NAFTA guidance documents are used. } \note{ The IORE submodel is not well tested for metabolites. When using this - model for metabolites, you may want to read the second note in the help - page to \code{\link{mkinfit}}. +model for metabolites, you may want to read the second note in the help +page to \code{\link{mkinfit}}. } \examples{ @@ -115,13 +120,13 @@ fit_DFOP_par_c <- mkinfit(m_synth_DFOP_par, } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} - NAFTA Technical Working Group on Pesticides (not dated) Guidance for - Evaluating and Calculating Degradation Kinetics in Environmental Media +NAFTA Technical Working Group on Pesticides (not dated) Guidance for +Evaluating and Calculating Degradation Kinetics in Environmental Media } \author{ Johannes Ranke diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd index 975a0203..07b25009 100644 --- a/man/mkinparplot.Rd +++ b/man/mkinparplot.Rd @@ -11,7 +11,7 @@ mkinparplot(object) } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the confidence intervals for the parameters fitted using diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd index 2a8b2d41..498d914d 100644 --- a/man/mkinresplot.Rd +++ b/man/mkinresplot.Rd @@ -54,7 +54,7 @@ be passed on to \code{\link{legend}}.} } \value{ Nothing is returned by this function, as it is called for its side - effect, namely to produce a plot. +effect, namely to produce a plot. } \description{ This function plots the residuals for the specified subset of the observed @@ -71,8 +71,8 @@ mkinresplot(fit, "m1") } \seealso{ \code{\link{mkinplot}}, for a way to plot the data and the fitted - lines of the mkinfit object, and \code{\link{plot_res}} for a function - combining the plot of the fit and the residual plot. +lines of the mkinfit object, and \code{\link{plot_res}} for a function +combining the plot of the fit and the residual plot. } \author{ Johannes Ranke diff --git a/man/mmkin.Rd b/man/mmkin.Rd index 99895400..eda0d837 100644 --- a/man/mmkin.Rd +++ b/man/mmkin.Rd @@ -33,8 +33,8 @@ for parallel execution.} } \value{ A two-dimensional \code{\link{array}} of \code{\link{mkinfit}} - objects that can be indexed using the model names for the first index (row index) - and the dataset names for the second index (column index). +objects that can be indexed using the model names for the first index (row index) +and the dataset names for the second index (column index). } \description{ This function calls \code{\link{mkinfit}} on all combinations of models and @@ -79,7 +79,7 @@ plot(fits.0[1, 1]) } \seealso{ \code{\link{[.mmkin}} for subsetting, \code{\link{plot.mmkin}} for - plotting. +plotting. } \author{ Johannes Ranke diff --git a/man/nafta.Rd b/man/nafta.Rd index 49c13afc..4f05324b 100644 --- a/man/nafta.Rd +++ b/man/nafta.Rd @@ -6,15 +6,15 @@ \title{Evaluate parent kinetics using the NAFTA guidance} \source{ NAFTA (2011) Guidance for evaluating and calculating degradation - kinetics in environmental media. NAFTA Technical Working Group on - Pesticides - \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} - accessed 2019-02-22 +kinetics in environmental media. NAFTA Technical Working Group on +Pesticides +\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/guidance-evaluating-and-calculating-degradation} +accessed 2019-02-22 - US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to - Calculate Representative Half-life Values and Characterizing Pesticide - Degradation - \url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} +US EPA (2015) Standard Operating Procedure for Using the NAFTA Guidance to +Calculate Representative Half-life Values and Characterizing Pesticide +Degradation +\url{https://www.epa.gov/pesticide-science-and-assessing-pesticide-risks/standard-operating-procedure-using-nafta-guidance} } \usage{ nafta(ds, title = NA, quiet = FALSE, ...) @@ -41,9 +41,9 @@ dissipation times.} } \value{ An list of class \code{nafta}. The list element named "mmkin" is the - \code{\link{mmkin}} object containing the fits of the three models. The - list element named "title" contains the title of the dataset used. The - list element "data" contains the dataset used in the fits. +\code{\link{mmkin}} object containing the fits of the three models. The +list element named "title" contains the title of the dataset used. The +list element "data" contains the dataset used in the fits. } \description{ The function fits the SFO, IORE and DFOP models using \code{\link{mmkin}} diff --git a/man/nlme.Rd b/man/nlme.Rd index a9e368dd..bf527320 100644 --- a/man/nlme.Rd +++ b/man/nlme.Rd @@ -21,9 +21,9 @@ nlme_data(object) A function that can be used with nlme If random is FALSE (default), a named vector containing mean values - of the fitted degradation model parameters. If random is TRUE, a list with - fixed and random effects, in the format required by the start argument of - nlme for the case of a single grouping variable ds? +of the fitted degradation model parameters. If random is TRUE, a list with +fixed and random effects, in the format required by the start argument of +nlme for the case of a single grouping variable ds? A \code{\link{groupedData}} object } diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 430dbda1..ae2b2d22 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -67,7 +67,7 @@ parameters taken from the mmkin object are used} } \value{ Upon success, a fitted nlme.mmkin object, which is an nlme object - with additional elements +with additional elements } \description{ This functions sets up a nonlinear mixed effects model for an mmkin row diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd index 4235557e..bf38c5a5 100644 --- a/man/plot.mkinfit.Rd +++ b/man/plot.mkinfit.Rd @@ -85,7 +85,7 @@ fits is shown, the residual plot is in the lower third of the plot. Otherwise, i.e. if "sep_obs" is given, the residual plots will be located to the right of the plots of the fitted curves. If this is set to 'standardized', a plot of the residuals divided by the standard deviation - given by the fitted error model will be shown.} +given by the fitted error model will be shown.} \item{show_errplot}{Should squared residuals and the error model be shown? If only one plot of the fits is shown, this plot is in the lower third of diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd index 600881ea..998e25e1 100644 --- a/man/plot.mmkin.Rd +++ b/man/plot.mmkin.Rd @@ -34,7 +34,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.} \item{standardized}{Should the residuals be standardized? This option is passed to \code{\link{mkinresplot}}, it only takes effect if -`resplot = "time"`.} +\code{resplot = "time"}.} \item{show_errmin}{Should the chi2 error level be shown on top of the plots to the left?} diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index 9bea7013..91130402 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -36,7 +36,7 @@ values, with the error model, using \code{\link{mkinerrplot}}.} \item{standardized}{Should the residuals be standardized? This option is passed to \code{\link{mkinresplot}}, it only takes effect if -`resplot = "time"`.} +\code{resplot = "time"}.} \item{show_errmin}{Should the chi2 error level be shown on top of the plots to the left?} diff --git a/man/sigma_twocomp.Rd b/man/sigma_twocomp.Rd index 0004144f..4e1f7c38 100644 --- a/man/sigma_twocomp.Rd +++ b/man/sigma_twocomp.Rd @@ -33,9 +33,9 @@ y. } \references{ Werner, Mario, Brooks, Samuel H., and Knott, Lancaster B. (1978) - Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry - 24(11), 1895-1898. +Additive, Multiplicative, and Mixed Analytical Errors. Clinical Chemistry +24(11), 1895-1898. - Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for - measurement error in analytical chemistry. Technometrics 37(2), 176-184. +Rocke, David M. and Lorenzato, Stefan (1995) A two-component model for +measurement error in analytical chemistry. Technometrics 37(2), 176-184. } diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd index fabe31d0..24991d71 100644 --- a/man/summary.mkinfit.Rd +++ b/man/summary.mkinfit.Rd @@ -29,27 +29,27 @@ distribution} } \value{ The summary function returns a list with components, among others - \item{version, Rversion}{The mkin and R versions used} - \item{date.fit, date.summary}{The dates where the fit and the summary were - produced} - \item{diffs}{The differential equations used in the model} - \item{use_of_ff}{Was maximum or minimum use made of formation fractions} - \item{bpar}{Optimised and backtransformed - parameters} - \item{data}{The data (see Description above).} - \item{start}{The starting values and bounds, if applicable, for optimised - parameters.} - \item{fixed}{The values of fixed parameters.} - \item{errmin }{The chi2 error levels for - each observed variable.} - \item{bparms.ode}{All backtransformed ODE - parameters, for use as starting parameters for related models.} - \item{errparms}{Error model parameters.} - \item{ff}{The estimated formation fractions derived from the fitted - model.} - \item{distimes}{The DT50 and DT90 values for each observed variable.} - \item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} - The print method is called for its side effect, i.e. printing the summary. +\item{version, Rversion}{The mkin and R versions used} +\item{date.fit, date.summary}{The dates where the fit and the summary were +produced} +\item{diffs}{The differential equations used in the model} +\item{use_of_ff}{Was maximum or minimum use made of formation fractions} +\item{bpar}{Optimised and backtransformed +parameters} +\item{data}{The data (see Description above).} +\item{start}{The starting values and bounds, if applicable, for optimised +parameters.} +\item{fixed}{The values of fixed parameters.} +\item{errmin }{The chi2 error levels for +each observed variable.} +\item{bparms.ode}{All backtransformed ODE +parameters, for use as starting parameters for related models.} +\item{errparms}{Error model parameters.} +\item{ff}{The estimated formation fractions derived from the fitted +model.} +\item{distimes}{The DT50 and DT90 values for each observed variable.} +\item{SFORB}{If applicable, eigenvalues of SFORB components of the model.} +The print method is called for its side effect, i.e. printing the summary. } \description{ Lists model equations, initial parameter values, optimised parameters with @@ -65,10 +65,10 @@ values. } \references{ 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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} +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://esdac.jrc.ec.europa.eu/projects/degradation-kinetics} } \author{ Johannes Ranke diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd index 5257fe12..e250483a 100644 --- a/man/transform_odeparms.Rd +++ b/man/transform_odeparms.Rd @@ -48,7 +48,7 @@ fitting procedure.} } \value{ A vector of transformed or backtransformed parameters with the same - names as the original parameters. +names as the original parameters. } \description{ The transformations are intended to map parameters that should only take on -- cgit v1.2.1