aboutsummaryrefslogtreecommitdiff
diff options
context:
space:
mode:
Diffstat
-rw-r--r--DESCRIPTION2
-rw-r--r--NAMESPACE3
-rw-r--r--R/memkin.R118
-rw-r--r--man/CAKE_export.Rd21
-rw-r--r--man/add_err.Rd12
-rw-r--r--man/confint.mkinfit.Rd17
-rw-r--r--man/lrtest.mkinfit.Rd2
-rw-r--r--man/memkin.Rd72
-rw-r--r--man/mkinds.Rd35
-rw-r--r--man/mkinerrplot.Rd19
-rw-r--r--man/mkinfit.Rd33
-rw-r--r--man/mkinmod.Rd9
-rw-r--r--man/mkinpredict.Rd57
-rw-r--r--man/mkinresplot.Rd18
-rw-r--r--man/mmkin.Rd11
-rw-r--r--man/plot.mkinfit.Rd55
-rw-r--r--man/plot.mmkin.Rd17
-rw-r--r--man/summary.mkinfit.Rd6
-rw-r--r--man/transform_odeparms.Rd16
19 files changed, 400 insertions, 123 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 0bc78ed2..bd6a0a09 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -27,4 +27,4 @@ Encoding: UTF-8
VignetteBuilder: knitr
BugReports: http://github.com/jranke/mkin/issues
URL: https://pkgdown.jrwb.de/mkin
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2
diff --git a/NAMESPACE b/NAMESPACE
index 26995055..5f9b360a 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -45,6 +45,7 @@ export(max_twa_fomc)
export(max_twa_hs)
export(max_twa_parent)
export(max_twa_sfo)
+export(memkin)
export(mkin_long_to_wide)
export(mkin_wide_to_long)
export(mkinds)
@@ -67,6 +68,7 @@ export(sigma_twocomp)
export(transform_odeparms)
import(deSolve)
import(graphics)
+import(nlme)
importFrom(R6,R6Class)
importFrom(grDevices,dev.cur)
importFrom(inline,cfunction)
@@ -76,6 +78,7 @@ importFrom(methods,signature)
importFrom(parallel,detectCores)
importFrom(parallel,mclapply)
importFrom(parallel,parLapply)
+importFrom(purrr,map_dfr)
importFrom(stats,AIC)
importFrom(stats,BIC)
importFrom(stats,aggregate)
diff --git a/R/memkin.R b/R/memkin.R
index 68837d86..5cc00345 100644
--- a/R/memkin.R
+++ b/R/memkin.R
@@ -6,9 +6,12 @@
#' datasets.
#'
#' @param object An mmkin row object containing several fits of the same model to different datasets
+#' @param random_spec Either "auto" or a specification of random effects for \code{\link{nlme}}
+#' given as a character vector
#' @param ... Additional arguments passed to \code{\link{nlme}}
-#' @importFrom nlme nlme
-#' @return A fitted object of class 'memkin'
+#' @import nlme
+#' @importFrom purrr map_dfr
+#' @return An nlme object
#' @examples
#' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
#' m_SFO <- mkinmod(parent = mkinsub("SFO"))
@@ -32,9 +35,44 @@
#'
#' f <- mmkin("SFO", ds)
#' x <- memkin(f)
+#' summary(x)
#'
+#' ds_2 <- lapply(experimental_data_for_UBA_2019[6:10],
+#' function(x) x$data[c("name", "time", "value")])
+#' m_sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
+#' A1 = mkinsub("SFO"), use_of_ff = "min")
+#' m_sfo_sfo_ff <- mkinmod(parent = mkinsub("SFO", "A1"),
+#' A1 = mkinsub("SFO"), use_of_ff = "max")
+#' m_fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
+#' A1 = mkinsub("SFO"))
+#' m_dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+#' A1 = mkinsub("SFO"))
+#' m_sforb_sfo <- mkinmod(parent = mkinsub("SFORB", "A1"),
+#' A1 = mkinsub("SFO"))
+#'
+#' f_2 <- mmkin(list("SFO-SFO" = m_sfo_sfo,
+#' "SFO-SFO-ff" = m_sfo_sfo_ff,
+#' "FOMC-SFO" = m_fomc_sfo,
+#' "DFOP-SFO" = m_dfop_sfo,
+#' "SFORB-SFO" = m_sforb_sfo),
+#' ds_2)
+#'
+#' f_nlme_sfo_sfo <- memkin(f_2[1, ])
+#' f_nlme_sfo_sfo_2 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 + log_k_A1_sink ~ 1)") # explicit
+#' f_nlme_sfo_sfo_3 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 ~ 1)") # reduced
+#' f_nlme_sfo_sfo_4 <- memkin(f_2[1, ], "pdDiag(parent_0 + log_k_parent_sink ~ 1)") # further reduced
+#' \dontrun{
+#' f_nlme_sfo_sfo_ff <- memkin(f_2[2, ]) # does not converge with maxIter = 50
+#' }
+#' f_nlme_fomc_sfo <- memkin(f_2[3, ])
+#' \dontrun{
+#' f_nlme_dfop_sfo <- memkin(f_2[4, ]) # apparently underdetermined}
+#' f_nlme_sforb_sfo <- memkin(f_2[5, ]) # also does not converge
+#' }
+#' anova(f_nlme_sfo_sfo, f_nlme_fomc_sfo)
+#' # The FOMC variant has a lower AIC and has significantly higher likelihood
#' @export
-memkin <- function(object, ...) {
+memkin <- function(object, random_spec = "auto", ...) {
if (nrow(object) > 1) stop("Only row objects allowed")
ds_names <- colnames(object)
@@ -47,6 +85,7 @@ memkin <- function(object, ...) {
ds_list <- lapply(object, function(x) x$data[c("time", "variable", "observed")])
names(ds_list) <- ds_names
ds_nlme <- purrr::map_dfr(ds_list, function(x) x, .id = "ds")
+ ds_nlme$variable <- as.character(ds_nlme$variable)
ds_nlme_grouped <- groupedData(observed ~ time | ds, ds_nlme)
mkin_model <- object[[1]]$mkinmod
@@ -56,22 +95,9 @@ memkin <- function(object, ...) {
model_function_alist <- replicate(length(p_names_mean_function) + 2, substitute())
names(model_function_alist) <- c("name", "time", p_names_mean_function)
-
-
- model_function_body <- quote({
- arg_frame <- as.data.frame(as.list((environment())))
- res <- parent_0 * exp( - exp(log_k_parent_sink) * time)
- dump(c("arg_frame", "res"), file = "out_1.txt", append = TRUE)
- return(res)
- })
- model_function <- as.function(c(model_function_alist, model_function_body))
- f_nlme <- eval(parse(text = nlme_call_text))
-
model_function_body <- quote({
- arg_frame <- as.data.frame(as.list((environment())))
-
+ arg_frame <- as.data.frame(as.list((environment())), stringsAsFactors = FALSE)
res_frame <- arg_frame[1:2]
-
parm_frame <- arg_frame[-(1:2)]
parms_unique <- unique(parm_frame)
@@ -87,45 +113,57 @@ memkin <- function(object, ...) {
}
res_list <- lapply(1:n_unique, function(x) {
- parms <- unlist(parms_unique[x, , drop = TRUE])
- odeini_parm_names <- grep('_0$', names(parms), value = TRUE)
- odeparm_names <- setdiff(names(parms), odeini_parm_names)
- odeini <- parms[odeini_parm_names]
- names(odeini) <- gsub('_0$', '', odeini_parm_names)
- odeparms <- backtransform_odeparms(parms[odeparm_names], mkin_model) # TBD rates/fractions
- out_wide <- mkinpredict(mkin_model, odeparms = odeparms,
- solution_type = "analytical",
- odeini = odeini, outtimes = unique(times_ds[[x]]))
+ transparms_optim <- unlist(parms_unique[x, , drop = TRUE])
+ parms_fixed <- object[[1]]$bparms.fixed
+
+ odeini_optim_parm_names <- grep('_0$', names(transparms_optim), value = TRUE)
+ odeini_optim <- transparms_optim[odeini_optim_parm_names]
+ names(odeini_optim) <- gsub('_0$', '', odeini_optim_parm_names)
+ odeini_fixed_parm_names <- grep('_0$', names(parms_fixed), value = TRUE)
+ odeini_fixed <- parms_fixed[odeini_fixed_parm_names]
+ names(odeini_fixed) <- gsub('_0$', '', odeini_fixed_parm_names)
+ odeini <- c(odeini_optim, odeini_fixed)[names(mkin_model$diffs)]
+
+ ode_transparms_optim_names <- setdiff(names(transparms_optim), odeini_optim_parm_names)
+ odeparms_optim <- backtransform_odeparms(transparms_optim[ode_transparms_optim_names], mkin_model,
+ transform_rates = object[[1]]$transform_rates,
+ transform_fractions = object[[1]]$transform_fractions)
+ odeparms_fixed_names <- setdiff(names(parms_fixed), odeini_fixed_parm_names)
+ odeparms_fixed <- parms_fixed[odeparms_fixed_names]
+ odeparms <- c(odeparms_optim, odeparms_fixed)
+
+ out_wide <- mkinpredict(mkin_model,
+ odeparms = odeparms, odeini = odeini,
+ solution_type = object[[1]]$solution_type,
+ outtimes = sort(unique(times_ds[[x]])))
out_array <- out_wide[, -1, drop = FALSE]
rownames(out_array) <- as.character(unique(times_ds[[x]]))
out_times <- as.character(times_ds[[x]])
- out_names <- names_ds[[x]]
+ out_names <- as.character(names_ds[[x]])
out_values <- mapply(function(times, names) out_array[times, names],
out_times, out_names)
return(as.numeric(out_values))
})
res <- unlist(res_list)
- #dump(c("arg_frame", "res"), file = "out_2.txt", append = TRUE)
return(res)
})
model_function <- as.function(c(model_function_alist, model_function_body))
- debug(model_function)
- f_nlme <- eval(parse(text = nlme_call_text))
-
- undebug(model_function)
-
- model_function(c(0, 0, 100), parent_0 = 100, log_k_parent_sink = log(0.1))
-
+ # For some reason, using envir = parent.frame() here is not enough,
+ # we need to use assign
+ assign("model_function", model_function, envir = parent.frame())
+
+ random_spec <- if (random_spec[1] == "auto") {
+ paste0("pdDiag(", paste(p_names_mean_function, collapse = " + "), " ~ 1),\n")
+ } else {
+ paste0(random_spec, ",\n")
+ }
nlme_call_text <- paste0(
"nlme(observed ~ model_function(variable, time, ",
paste(p_names_mean_function, collapse = ", "), "),\n",
" data = ds_nlme_grouped,\n",
" fixed = ", paste(p_names_mean_function, collapse = " + "), " ~ 1,\n",
- " random = pdDiag(", paste(p_names_mean_function, collapse = " + "), " ~ 1),\n",
- #" start = c(parent_0 = 100, log_k_parent_sink = log(0.1)), verbose = TRUE)\n")
- #" start = p_start_mean_function)\n")
- " start = p_start_mean_function, verbose = TRUE)\n")
- cat(nlme_call_text)
+ " random = ", random_spec, "\n",
+ " start = p_start_mean_function)\n")
f_nlme <- eval(parse(text = nlme_call_text))
diff --git a/man/CAKE_export.Rd b/man/CAKE_export.Rd
index 142b4a75..4bcd8581 100644
--- a/man/CAKE_export.Rd
+++ b/man/CAKE_export.Rd
@@ -4,12 +4,21 @@
\alias{CAKE_export}
\title{Export a list of datasets format to a CAKE study file}
\usage{
-CAKE_export(ds, map = c(parent = "Parent"), links = NA,
- filename = "CAKE_export.csf", path = ".", overwrite = FALSE,
- study = "Codlemone aerobic soil degradation", description = "",
- time_unit = "days", res_unit = "\% AR",
- comment = "Created using mkin::CAKE_export", date = Sys.Date(),
- optimiser = "IRLS")
+CAKE_export(
+ ds,
+ map = c(parent = "Parent"),
+ links = NA,
+ filename = "CAKE_export.csf",
+ path = ".",
+ overwrite = FALSE,
+ study = "Codlemone aerobic soil degradation",
+ description = "",
+ time_unit = "days",
+ res_unit = "\% AR",
+ comment = "Created using mkin::CAKE_export",
+ date = Sys.Date(),
+ optimiser = "IRLS"
+)
}
\arguments{
\item{ds}{A named list of datasets in long format as compatible with
diff --git a/man/add_err.Rd b/man/add_err.Rd
index 36b98be9..3452923e 100644
--- a/man/add_err.Rd
+++ b/man/add_err.Rd
@@ -4,8 +4,16 @@
\alias{add_err}
\title{Add normally distributed errors to simulated kinetic degradation data}
\usage{
-add_err(prediction, sdfunc, secondary = c("M1", "M2"), n = 1000,
- LOD = 0.1, reps = 2, digits = 1, seed = NA)
+add_err(
+ prediction,
+ sdfunc,
+ secondary = c("M1", "M2"),
+ n = 1000,
+ LOD = 0.1,
+ reps = 2,
+ digits = 1,
+ seed = NA
+)
}
\arguments{
\item{prediction}{A prediction from a kinetic model as produced by
diff --git a/man/confint.mkinfit.Rd b/man/confint.mkinfit.Rd
index f2521ccd..81d7a6e8 100644
--- a/man/confint.mkinfit.Rd
+++ b/man/confint.mkinfit.Rd
@@ -4,10 +4,19 @@
\alias{confint.mkinfit}
\title{Confidence intervals for parameters of mkinfit objects}
\usage{
-\method{confint}{mkinfit}(object, parm, level = 0.95, alpha = 1 -
- level, cutoff, method = c("quadratic", "profile"),
- transformed = TRUE, backtransform = TRUE,
- cores = round(detectCores()/2), quiet = FALSE, ...)
+\method{confint}{mkinfit}(
+ object,
+ parm,
+ level = 0.95,
+ alpha = 1 - level,
+ cutoff,
+ method = c("quadratic", "profile"),
+ transformed = TRUE,
+ backtransform = TRUE,
+ cores = round(detectCores()/2),
+ quiet = FALSE,
+ ...
+)
}
\arguments{
\item{object}{An \code{\link{mkinfit}} object}
diff --git a/man/lrtest.mkinfit.Rd b/man/lrtest.mkinfit.Rd
index 84d7bc99..8025b883 100644
--- a/man/lrtest.mkinfit.Rd
+++ b/man/lrtest.mkinfit.Rd
@@ -47,7 +47,7 @@ lrtest(sfo_fit, dfop_fit)
#lrtest(dfop_fit, error_model = "tc")
#lrtest(dfop_fit, fixed_parms = c(k2 = 0))
-# However, this equivalent syntax works for static help pages
+# However, this equivalent syntax also works for static help pages
lrtest(dfop_fit, update(dfop_fit, error_model = "tc"))
lrtest(dfop_fit, update(dfop_fit, fixed_parms = c(k2 = 0)))
}
diff --git a/man/memkin.Rd b/man/memkin.Rd
new file mode 100644
index 00000000..cda9b468
--- /dev/null
+++ b/man/memkin.Rd
@@ -0,0 +1,72 @@
+% Generated by roxygen2: do not edit by hand
+% Please edit documentation in R/memkin.R
+\name{memkin}
+\alias{memkin}
+\title{Estimation of parameter distributions from mmkin row objects}
+\usage{
+memkin(object, ...)
+}
+\arguments{
+\item{object}{An mmkin row object containing several fits of the same model to different datasets}
+
+\item{...}{Additional arguments passed to \code{\link{nlme}}}
+}
+\value{
+A fitted object of class 'memkin'
+}
+\description{
+This function sets up and attempts to fit a mixed effects model to
+an mmkin row object which is essentially a list of mkinfit objects
+that have been obtained by fitting the same model to a list of
+datasets.
+}
+\examples{
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+m_SFO <- mkinmod(parent = mkinsub("SFO"))
+d_SFO_1 <- mkinpredict(m_SFO,
+ c(k_parent_sink = 0.1),
+ c(parent = 98), sampling_times)
+d_SFO_1_long <- mkin_wide_to_long(d_SFO_1, time = "time")
+d_SFO_2 <- mkinpredict(m_SFO,
+ c(k_parent_sink = 0.05),
+ c(parent = 102), sampling_times)
+d_SFO_2_long <- mkin_wide_to_long(d_SFO_2, time = "time")
+d_SFO_3 <- mkinpredict(m_SFO,
+ c(k_parent_sink = 0.02),
+ c(parent = 103), sampling_times)
+d_SFO_3_long <- mkin_wide_to_long(d_SFO_3, time = "time")
+
+d1 <- add_err(d_SFO_1, function(value) 3, n = 1)
+d2 <- add_err(d_SFO_2, function(value) 2, n = 1)
+d3 <- add_err(d_SFO_3, function(value) 4, n = 1)
+ds <- c(d1 = d1, d2 = d2, d3 = d3)
+
+f <- mmkin("SFO", ds)
+x <- memkin(f)
+summary(x)
+
+ds_2 <- lapply(experimental_data_for_UBA_2019[6:10],
+ function(x) x$data[c("name", "time", "value")])
+m_sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"),
+ A1 = mkinsub("SFO"), use_of_ff = "min")
+m_sfo_sfo_ff <- mkinmod(parent = mkinsub("SFO", "A1"),
+ A1 = mkinsub("SFO"), use_of_ff = "max")
+m_fomc_sfo <- mkinmod(parent = mkinsub("FOMC", "A1"),
+ A1 = mkinsub("SFO"))
+m_dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"),
+ A1 = mkinsub("SFO"))
+
+f_2 <- mmkin(list("SFO-SFO" = m_sfo_sfo,
+ "SFO-SFO-ff" = m_sfo_sfo_ff,
+ "FOMC-SFO" = m_fomc_sfo,
+ "DFOP-SFO" = m_dfop_sfo),
+ ds_2)
+
+f_nlme_sfo_sfo <- memkin(f_2[1, ])
+\dontrun{f_nlme_sfo_sfo_ff <- memkin(f_2[2, ])} # does not converge with maxIter = 50
+f_nlme_fomc_sfo <- memkin(f_2[3, ])
+\dontrun{f_nlme_dfop_sfo <- memkin(f_2[4, ]) # apparently underdetermined}
+anova(f_nlme_sfo_sfo, f_nlme_fomc_sfo)
+# The FOMC variant has a lower AIC and has significantly higher likelihood
+update(f_nlme_fomc_sfo)
+}
diff --git a/man/mkinds.Rd b/man/mkinds.Rd
index 0ea562ed..79eb0167 100644
--- a/man/mkinds.Rd
+++ b/man/mkinds.Rd
@@ -5,9 +5,6 @@
\alias{mkinds}
\title{A dataset class for mkin}
\format{An \code{\link{R6Class}} generator object.}
-\usage{
-mkinds
-}
\description{
A dataset class for mkin
}
@@ -36,3 +33,35 @@ mds <- mkinds$new("FOCUS A", FOCUS_2006_A)
}
\keyword{datasets}
+\section{Methods}{
+\subsection{Public methods}{
+\itemize{
+\item \href{#method-new}{\code{mkinds$new()}}
+\item \href{#method-clone}{\code{mkinds$clone()}}
+}
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-new"></a>}}
+\subsection{Method \code{new()}}{
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{mkinds$new(title = "", data, time_unit = NA, unit = NA)}\if{html}{\out{</div>}}
+}
+
+}
+\if{html}{\out{<hr>}}
+\if{html}{\out{<a id="method-clone"></a>}}
+\subsection{Method \code{clone()}}{
+The objects of this class are cloneable with this method.
+\subsection{Usage}{
+\if{html}{\out{<div class="r">}}\preformatted{mkinds$clone(deep = FALSE)}\if{html}{\out{</div>}}
+}
+
+\subsection{Arguments}{
+\if{html}{\out{<div class="arguments">}}
+\describe{
+\item{\code{deep}}{Whether to make a deep clone.}
+}
+\if{html}{\out{</div>}}
+}
+}
+}
diff --git a/man/mkinerrplot.Rd b/man/mkinerrplot.Rd
index 3c53e7f8..9564ec19 100644
--- a/man/mkinerrplot.Rd
+++ b/man/mkinerrplot.Rd
@@ -4,11 +4,20 @@
\alias{mkinerrplot}
\title{Function to plot squared residuals and the error model for an mkin object}
\usage{
-mkinerrplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
- 1.1 * max(object$data$predicted)), xlab = "Predicted",
- ylab = "Squared residual", maxy = "auto", legend = TRUE,
- lpos = "topright", col_obs = "auto", pch_obs = "auto",
- frame = TRUE, ...)
+mkinerrplot(
+ object,
+ obs_vars = names(object$mkinmod$map),
+ xlim = c(0, 1.1 * max(object$data$predicted)),
+ xlab = "Predicted",
+ ylab = "Squared residual",
+ maxy = "auto",
+ legend = TRUE,
+ lpos = "topright",
+ col_obs = "auto",
+ pch_obs = "auto",
+ frame = TRUE,
+ ...
+)
}
\arguments{
\item{object}{A fit represented in an \code{\link{mkinfit}} object.}
diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index e58e61e2..45036361 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -8,18 +8,33 @@ 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, observed, parms.ini = "auto", state.ini = "auto",
- err.ini = "auto", fixed_parms = NULL,
- fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE,
+mkinfit(
+ mkinmod,
+ observed,
+ parms.ini = "auto",
+ state.ini = "auto",
+ err.ini = "auto",
+ fixed_parms = NULL,
+ fixed_initials = names(mkinmod$diffs)[-1],
+ from_max_mean = FALSE,
solution_type = c("auto", "analytical", "eigen", "deSolve"),
- method.ode = "lsoda", use_compiled = "auto",
+ method.ode = "lsoda",
+ use_compiled = "auto",
control = list(eval.max = 300, iter.max = 200),
- transform_rates = TRUE, transform_fractions = TRUE, quiet = FALSE,
- atol = 1e-08, rtol = 1e-10, n.outtimes = 100,
+ transform_rates = TRUE,
+ transform_fractions = TRUE,
+ quiet = FALSE,
+ atol = 1e-08,
+ rtol = 1e-10,
+ n.outtimes = 100,
error_model = c("const", "obs", "tc"),
- error_model_algorithm = c("auto", "d_3", "direct", "twostep",
- "threestep", "fourstep", "IRLS", "OLS"), reweight.tol = 1e-08,
- reweight.max.iter = 10, trace_parms = FALSE, ...)
+ error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep",
+ "IRLS", "OLS"),
+ reweight.tol = 1e-08,
+ reweight.max.iter = 10,
+ trace_parms = FALSE,
+ ...
+)
}
\arguments{
\item{mkinmod}{A list of class \code{\link{mkinmod}}, containing the kinetic
diff --git a/man/mkinmod.Rd b/man/mkinmod.Rd
index 91f285e2..d2b851b6 100644
--- a/man/mkinmod.Rd
+++ b/man/mkinmod.Rd
@@ -4,8 +4,13 @@
\alias{mkinmod}
\title{Function to set up a kinetic model with one or more state variables}
\usage{
-mkinmod(..., use_of_ff = "min", speclist = NULL, quiet = FALSE,
- verbose = FALSE)
+mkinmod(
+ ...,
+ use_of_ff = "min",
+ speclist = NULL,
+ quiet = FALSE,
+ verbose = FALSE
+)
}
\arguments{
\item{...}{For each observed variable, a list has to be specified as an
diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd
index 53f02dea..17d7ef21 100644
--- a/man/mkinpredict.Rd
+++ b/man/mkinpredict.Rd
@@ -6,22 +6,47 @@
\alias{mkinpredict.mkinfit}
\title{Produce predictions from a kinetic model using specific parameters}
\usage{
-mkinpredict(x, odeparms, odeini, outtimes = seq(0, 120, by = 0.1),
- solution_type = "deSolve", use_compiled = "auto",
- method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
- map_output = TRUE, ...)
-
-\method{mkinpredict}{mkinmod}(x, odeparms = c(k_parent_sink = 0.1),
- odeini = c(parent = 100), outtimes = seq(0, 120, by = 0.1),
- solution_type = "deSolve", use_compiled = "auto",
- method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
- map_output = TRUE, ...)
-
-\method{mkinpredict}{mkinfit}(x, odeparms = x$bparms.ode,
- odeini = x$bparms.state, outtimes = seq(0, 120, by = 0.1),
- solution_type = "deSolve", use_compiled = "auto",
- method.ode = "lsoda", atol = 1e-08, rtol = 1e-10,
- map_output = TRUE, ...)
+mkinpredict(
+ x,
+ odeparms,
+ odeini,
+ outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve",
+ use_compiled = "auto",
+ method.ode = "lsoda",
+ atol = 1e-08,
+ rtol = 1e-10,
+ map_output = TRUE,
+ ...
+)
+
+\method{mkinpredict}{mkinmod}(
+ x,
+ odeparms = c(k_parent_sink = 0.1),
+ odeini = c(parent = 100),
+ outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve",
+ use_compiled = "auto",
+ method.ode = "lsoda",
+ atol = 1e-08,
+ rtol = 1e-10,
+ map_output = TRUE,
+ ...
+)
+
+\method{mkinpredict}{mkinfit}(
+ x,
+ odeparms = x$bparms.ode,
+ odeini = x$bparms.state,
+ outtimes = seq(0, 120, by = 0.1),
+ solution_type = "deSolve",
+ use_compiled = "auto",
+ method.ode = "lsoda",
+ atol = 1e-08,
+ rtol = 1e-10,
+ map_output = TRUE,
+ ...
+)
}
\arguments{
\item{x}{A kinetic model as produced by \code{\link{mkinmod}}, or a kinetic
diff --git a/man/mkinresplot.Rd b/man/mkinresplot.Rd
index 465b3038..2a8b2d41 100644
--- a/man/mkinresplot.Rd
+++ b/man/mkinresplot.Rd
@@ -4,11 +4,21 @@
\alias{mkinresplot}
\title{Function to plot residuals stored in an mkin object}
\usage{
-mkinresplot(object, obs_vars = names(object$mkinmod$map), xlim = c(0,
- 1.1 * max(object$data$time)), standardized = FALSE, xlab = "Time",
+mkinresplot(
+ object,
+ obs_vars = names(object$mkinmod$map),
+ xlim = c(0, 1.1 * max(object$data$time)),
+ standardized = FALSE,
+ xlab = "Time",
ylab = ifelse(standardized, "Standardized residual", "Residual"),
- maxabs = "auto", legend = TRUE, lpos = "topright",
- col_obs = "auto", pch_obs = "auto", frame = TRUE, ...)
+ maxabs = "auto",
+ legend = TRUE,
+ lpos = "topright",
+ col_obs = "auto",
+ pch_obs = "auto",
+ frame = TRUE,
+ ...
+)
}
\arguments{
\item{object}{A fit represented in an \code{\link{mkinfit}} object.}
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index a763fcdf..4bf07370 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -5,11 +5,16 @@
\title{Fit one or more kinetic models with one or more state variables to one or
more datasets}
\usage{
-mmkin(models = c("SFO", "FOMC", "DFOP"), datasets,
- cores = round(detectCores()/2), cluster = NULL, ...)
+mmkin(
+ models = c("SFO", "FOMC", "DFOP"),
+ datasets,
+ cores = round(detectCores()/2),
+ cluster = NULL,
+ ...
+)
}
\arguments{
-\item{models}{Either a character vector of shorthand names like
+\item{models}{Either a character vector of shorthand names like
\code{c("SFO", "FOMC", "DFOP", "HS", "SFORB")}, or an optionally named
list of \code{\link{mkinmod}} objects.}
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 47cc08a4..c3f3134a 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -7,22 +7,47 @@
\alias{plot_err}
\title{Plot the observed data and the fitted model of an mkinfit object}
\usage{
-\method{plot}{mkinfit}(x, fit = x, obs_vars = names(fit$mkinmod$map),
- xlab = "Time", ylab = "Observed", xlim = range(fit$data$time),
- ylim = "default", col_obs = 1:length(obs_vars), pch_obs = col_obs,
- lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add,
- show_residuals = FALSE, show_errplot = FALSE, maxabs = "auto",
- sep_obs = FALSE, rel.height.middle = 0.9, row_layout = FALSE,
- lpos = "topright", inset = c(0.05, 0.05), show_errmin = FALSE,
- errmin_digits = 3, frame = TRUE, ...)
-
-plot_sep(fit, show_errmin = TRUE,
- show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE,
- "standardized"), ...)
-
-plot_res(fit, sep_obs = FALSE, show_errmin = sep_obs,
+\method{plot}{mkinfit}(
+ x,
+ fit = x,
+ obs_vars = names(fit$mkinmod$map),
+ xlab = "Time",
+ ylab = "Observed",
+ xlim = range(fit$data$time),
+ ylim = "default",
+ col_obs = 1:length(obs_vars),
+ pch_obs = col_obs,
+ lty_obs = rep(1, length(obs_vars)),
+ add = FALSE,
+ legend = !add,
+ show_residuals = FALSE,
+ show_errplot = FALSE,
+ maxabs = "auto",
+ sep_obs = FALSE,
+ rel.height.middle = 0.9,
+ row_layout = FALSE,
+ lpos = "topright",
+ inset = c(0.05, 0.05),
+ show_errmin = FALSE,
+ errmin_digits = 3,
+ frame = TRUE,
+ ...
+)
+
+plot_sep(
+ fit,
+ show_errmin = TRUE,
+ show_residuals = ifelse(identical(fit$err_mod, "const"), TRUE, "standardized"),
+ ...
+)
+
+plot_res(
+ fit,
+ sep_obs = FALSE,
+ show_errmin = sep_obs,
standardized = ifelse(identical(fit$err_mod, "const"), FALSE, TRUE),
- ...)
+ ...
+)
plot_err(fit, sep_obs = FALSE, show_errmin = sep_obs, ...)
}
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 605e458e..f14e0362 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -5,10 +5,19 @@
\title{Plot model fits (observed and fitted) and the residuals for a row or column
of an mmkin object}
\usage{
-\method{plot}{mmkin}(x, main = "auto", legends = 1,
- resplot = c("time", "errmod"), show_errmin = TRUE,
- errmin_var = "All data", errmin_digits = 3, cex = 0.7,
- rel.height.middle = 0.9, ymax = "auto", ...)
+\method{plot}{mmkin}(
+ x,
+ main = "auto",
+ legends = 1,
+ resplot = c("time", "errmod"),
+ show_errmin = TRUE,
+ errmin_var = "All data",
+ errmin_digits = 3,
+ cex = 0.7,
+ rel.height.middle = 0.9,
+ ymax = "auto",
+ ...
+)
}
\arguments{
\item{x}{An object of class \code{\link{mmkin}}, with either one row or one
diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index fcc1295f..fabe31d0 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -5,11 +5,9 @@
\alias{print.summary.mkinfit}
\title{Summary method for class "mkinfit"}
\usage{
-\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE,
- alpha = 0.05, ...)
+\method{summary}{mkinfit}(object, data = TRUE, distimes = TRUE, alpha = 0.05, ...)
-\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") -
- 3), ...)
+\method{print}{summary.mkinfit}(x, digits = max(3, getOption("digits") - 3), ...)
}
\arguments{
\item{object}{an object of class \code{\link{mkinfit}}.}
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 5c8c90ba..5257fe12 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -5,11 +5,19 @@
\alias{backtransform_odeparms}
\title{Functions to transform and backtransform kinetic parameters for fitting}
\usage{
-transform_odeparms(parms, mkinmod, transform_rates = TRUE,
- transform_fractions = TRUE)
+transform_odeparms(
+ parms,
+ mkinmod,
+ transform_rates = TRUE,
+ transform_fractions = TRUE
+)
-backtransform_odeparms(transparms, mkinmod, transform_rates = TRUE,
- transform_fractions = TRUE)
+backtransform_odeparms(
+ transparms,
+ mkinmod,
+ transform_rates = TRUE,
+ transform_fractions = TRUE
+)
}
\arguments{
\item{parms}{Parameters of kinetic models as used in the differential

Contact - Imprint