From f0ef23a7598e5d19648ae4edc2b74e0fba27a41c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 3 Feb 2021 16:41:31 +0100 Subject: Prepare for v1.0.0 - Improve authorship and copyright information - Prepare pkgdown config - Remove dependence on saemix as we need the development version which is not ready for CRAN - Temporarily remove saemix interface to check code coverage of the rest --- man/endpoints.Rd | 8 +-- man/plot.mixed.mmkin.Rd | 13 +--- man/saem.Rd | 155 ---------------------------------------------- man/summary.saem.mmkin.Rd | 100 ------------------------------ 4 files changed, 6 insertions(+), 270 deletions(-) delete mode 100644 man/saem.Rd delete mode 100644 man/summary.saem.mmkin.Rd (limited to 'man') diff --git a/man/endpoints.Rd b/man/endpoints.Rd index 72487717..0b225e62 100644 --- a/man/endpoints.Rd +++ b/man/endpoints.Rd @@ -8,8 +8,8 @@ with mkinfit} endpoints(fit) } \arguments{ -\item{fit}{An object of class \link{mkinfit}, \link{nlme.mmkin} or -\link{saem.mmkin}. Or another object that has list components +\item{fit}{An object of class \link{mkinfit} or \link{nlme.mmkin} +or another object that has list components mkinmod containing an \link{mkinmod} degradation model, and two numeric vectors, bparms.optim and bparms.fixed, that contain parameter values for that model.} @@ -32,8 +32,8 @@ Additional DT50 values are calculated from the FOMC DT90 and k1 and k2 from HS and DFOP, as well as from Eigenvalues b1 and b2 of any SFORB models } \note{ -The function is used internally by \link{summary.mkinfit}, -\link{summary.nlme.mmkin} and \link{summary.saem.mmkin}. +The function is used internally by \link{summary.mkinfit} +and \link{summary.nlme.mmkin} } \examples{ diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd index c7b2344f..87a82286 100644 --- a/man/plot.mixed.mmkin.Rd +++ b/man/plot.mixed.mmkin.Rd @@ -17,7 +17,7 @@ maxabs = "auto", ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), nrow.legend = ceiling((length(i) + 1)/ncol.legend), - rel.height.legend = 0.03 + 0.08 * nrow.legend, + rel.height.legend = 0.02 + 0.07 * nrow.legend, rel.height.bottom = 1.1, pch_ds = 1:length(i), col_ds = pch_ds + 1, @@ -27,7 +27,7 @@ ) } \arguments{ -\item{x}{An object of class \link{mixed.mmkin}, \link{saem.mmkin} or \link{nlme.mmkin}} +\item{x}{An object of class \link{mixed.mmkin}, \link{nlme.mmkin}} \item{i}{A numeric index to select datasets for which to plot the individual predictions, in case plots get too large} @@ -94,15 +94,6 @@ plot(f[, 3:4], standardized = TRUE) f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) plot(f_nlme) -f_saem <- saem(f, transformations = "saemix") -plot(f_saem) - -# We can overlay the two variants if we generate predictions -pred_nlme <- mkinpredict(dfop_sfo, - f_nlme$bparms.optim[-1], - c(parent = f_nlme$bparms.optim[[1]], A1 = 0), - seq(0, 180, by = 0.2)) -plot(f_saem, pred_over = list(nlme = pred_nlme)) } } \author{ diff --git a/man/saem.Rd b/man/saem.Rd deleted file mode 100644 index d5a8f17e..00000000 --- a/man/saem.Rd +++ /dev/null @@ -1,155 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/saem.R -\name{saem} -\alias{saem} -\alias{saem.mmkin} -\alias{print.saem.mmkin} -\alias{saemix_model} -\alias{saemix_data} -\title{Fit nonlinear mixed models with SAEM} -\usage{ -saem(object, ...) - -\method{saem}{mmkin}( - object, - transformations = c("mkin", "saemix"), - degparms_start = numeric(), - solution_type = "auto", - control = list(displayProgress = FALSE, print = FALSE, save = FALSE, save.graphs = - FALSE), - verbose = FALSE, - quiet = FALSE, - ... -) - -\method{print}{saem.mmkin}(x, digits = max(3, getOption("digits") - 3), ...) - -saemix_model( - object, - solution_type = "auto", - transformations = c("mkin", "saemix"), - degparms_start = numeric(), - verbose = FALSE, - ... -) - -saemix_data(object, verbose = FALSE, ...) -} -\arguments{ -\item{object}{An \link{mmkin} row object containing several fits of the same -\link{mkinmod} model to different datasets} - -\item{\dots}{Further parameters passed to \link[saemix:saemixModel]{saemix::saemixModel}.} - -\item{transformations}{Per default, all parameter transformations are done -in mkin. If this argument is set to 'saemix', parameter transformations -are done in 'saemix' for the supported cases. Currently this is only -supported in cases where the initial concentration of the parent is not fixed, -SFO or DFOP is used for the parent and there is either no metabolite or one.} - -\item{degparms_start}{Parameter values given as a named numeric vector will -be used to override the starting values obtained from the 'mmkin' object.} - -\item{solution_type}{Possibility to specify the solution type in case the -automatic choice is not desired} - -\item{control}{Passed to \link[saemix:saemix]{saemix::saemix}} - -\item{verbose}{Should we print information about created objects of -type \link[saemix:SaemixModel-class]{saemix::SaemixModel} and \link[saemix:SaemixData-class]{saemix::SaemixData}?} - -\item{quiet}{Should we suppress the messages saemix prints at the beginning -and the end of the optimisation process?} - -\item{x}{An saem.mmkin object to print} - -\item{digits}{Number of digits to use for printing} -} -\value{ -An S3 object of class 'saem.mmkin', containing the fitted -\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The -object also inherits from 'mixed.mmkin'. - -An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object. - -An \link[saemix:SaemixData-class]{saemix::SaemixData} object. -} -\description{ -This function uses \code{\link[saemix:saemix]{saemix::saemix()}} as a backend for fitting nonlinear mixed -effects models created from \link{mmkin} row objects using the Stochastic Approximation -Expectation Maximisation algorithm (SAEM). -} -\details{ -An mmkin row object is essentially a list of mkinfit objects that have been -obtained by fitting the same model to a list of datasets using \link{mkinfit}. - -Starting values for the fixed effects (population mean parameters, argument -psi0 of \code{\link[saemix:saemixModel]{saemix::saemixModel()}} are the mean values of the parameters found -using \link{mmkin}. -} -\examples{ -\dontrun{ -ds <- lapply(experimental_data_for_UBA_2019[6:10], - function(x) subset(x$data[c("name", "time", "value")])) -names(ds) <- paste("Dataset", 6:10) -f_mmkin_parent_p0_fixed <- mmkin("FOMC", ds, - state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE) -f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed) - -f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE) -f_saem_sfo <- saem(f_mmkin_parent["SFO", ]) -f_saem_fomc <- saem(f_mmkin_parent["FOMC", ]) -f_saem_dfop <- saem(f_mmkin_parent["DFOP", ]) - -# The returned saem.mmkin object contains an SaemixObject, therefore we can use -# functions from saemix -library(saemix) -compare.saemix(list(f_saem_sfo$so, f_saem_fomc$so, f_saem_dfop$so)) -plot(f_saem_fomc$so, plot.type = "convergence") -plot(f_saem_fomc$so, plot.type = "individual.fit") -plot(f_saem_fomc$so, plot.type = "npde") -plot(f_saem_fomc$so, plot.type = "vpc") - -f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc") -f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ]) -compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so)) - -sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), - A1 = mkinsub("SFO")) -fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"), - A1 = mkinsub("SFO")) -dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), - A1 = mkinsub("SFO")) -# The following fit uses analytical solutions for SFO-SFO and DFOP-SFO, -# and compiled ODEs for FOMC that are much slower -f_mmkin <- mmkin(list( - "SFO-SFO" = sfo_sfo, "FOMC-SFO" = fomc_sfo, "DFOP-SFO" = dfop_sfo), - ds, quiet = TRUE) -# saem fits of SFO-SFO and DFOP-SFO to these data take about five seconds -# each on this system, as we use analytical solutions written for saemix. -# When using the analytical solutions written for mkin this took around -# four minutes -f_saem_sfo_sfo <- saem(f_mmkin["SFO-SFO", ]) -f_saem_dfop_sfo <- saem(f_mmkin["DFOP-SFO", ]) -# We can use print, plot and summary methods to check the results -print(f_saem_dfop_sfo) -plot(f_saem_dfop_sfo) -summary(f_saem_dfop_sfo, data = TRUE) - -# The following takes about 6 minutes -#f_saem_dfop_sfo_deSolve <- saem(f_mmkin["DFOP-SFO", ], solution_type = "deSolve", -# control = list(nbiter.saemix = c(200, 80), nbdisplay = 10)) - -#saemix::compare.saemix(list( -# f_saem_dfop_sfo$so, -# f_saem_dfop_sfo_deSolve$so)) - -# If the model supports it, we can also use eigenvalue based solutions, which -# take a similar amount of time -#f_saem_sfo_sfo_eigen <- saem(f_mmkin["SFO-SFO", ], solution_type = "eigen", -# control = list(nbiter.saemix = c(200, 80), nbdisplay = 10)) -} -} -\seealso{ -\link{summary.saem.mmkin} \link{plot.mixed.mmkin} -} diff --git a/man/summary.saem.mmkin.Rd b/man/summary.saem.mmkin.Rd deleted file mode 100644 index 67cb3cbb..00000000 --- a/man/summary.saem.mmkin.Rd +++ /dev/null @@ -1,100 +0,0 @@ -% Generated by roxygen2: do not edit by hand -% Please edit documentation in R/summary.saem.mmkin.R -\name{summary.saem.mmkin} -\alias{summary.saem.mmkin} -\alias{print.summary.saem.mmkin} -\title{Summary method for class "saem.mmkin"} -\usage{ -\method{summary}{saem.mmkin}(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...) - -\method{print}{summary.saem.mmkin}(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...) -} -\arguments{ -\item{object}{an object of class \link{saem.mmkin}} - -\item{data}{logical, indicating whether the full data should be included in -the summary.} - -\item{verbose}{Should the summary be verbose?} - -\item{distimes}{logical, indicating whether DT50 and DT90 values should be -included.} - -\item{\dots}{optional arguments passed to methods like \code{print}.} - -\item{x}{an object of class \link{summary.saem.mmkin}} - -\item{digits}{Number of digits to use for printing} -} -\value{ -The summary function returns a list based on the \link[saemix:SaemixObject-class]{saemix::SaemixObject} -obtained in the fit, with at least the following additional components -\item{saemixversion, mkinversion, Rversion}{The saemix, 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 degradation model} -\item{use_of_ff}{Was maximum or minimum use made of formation fractions} -\item{data}{The data} -\item{confint_trans}{Transformed parameters as used in the optimisation, with confidence intervals} -\item{confint_back}{Backtransformed parameters, with confidence intervals if available} -\item{confint_errmod}{Error model parameters with confidence intervals} -\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 -for fixed effects (population), random effects (deviations from the -population mean) and residual error model, as well as the resulting -endpoints such as formation fractions and DT50 values. Optionally -(default is FALSE), the data are listed in full. -} -\examples{ -# Generate five datasets following DFOP-SFO kinetics -sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "m1"), - m1 = mkinsub("SFO"), quiet = TRUE) -set.seed(1234) -k1_in <- rlnorm(5, log(0.1), 0.3) -k2_in <- rlnorm(5, log(0.02), 0.3) -g_in <- plogis(rnorm(5, qlogis(0.5), 0.3)) -f_parent_to_m1_in <- plogis(rnorm(5, qlogis(0.3), 0.3)) -k_m1_in <- rlnorm(5, log(0.02), 0.3) - -pred_dfop_sfo <- function(k1, k2, g, f_parent_to_m1, k_m1) { - mkinpredict(dfop_sfo, - c(k1 = k1, k2 = k2, g = g, f_parent_to_m1 = f_parent_to_m1, k_m1 = k_m1), - c(parent = 100, m1 = 0), - sampling_times) -} - -ds_mean_dfop_sfo <- lapply(1:5, function(i) { - mkinpredict(dfop_sfo, - c(k1 = k1_in[i], k2 = k2_in[i], g = g_in[i], - f_parent_to_m1 = f_parent_to_m1_in[i], k_m1 = k_m1_in[i]), - c(parent = 100, m1 = 0), - sampling_times) -}) -names(ds_mean_dfop_sfo) <- paste("ds", 1:5) - -ds_syn_dfop_sfo <- lapply(ds_mean_dfop_sfo, function(ds) { - add_err(ds, - sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), - n = 1)[[1]] -}) - -\dontrun{ -# Evaluate using mmkin and saem -f_mmkin_dfop_sfo <- mmkin(list(dfop_sfo), ds_syn_dfop_sfo, - quiet = TRUE, error_model = "tc", cores = 5) -f_saem_dfop_sfo <- saem(f_mmkin_dfop_sfo) -summary(f_saem_dfop_sfo, data = TRUE) -} - -} -\author{ -Johannes Ranke for the mkin specific parts -saemix authors for the parts inherited from saemix. -} -- cgit v1.2.1