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-rw-r--r--DESCRIPTION2
-rw-r--r--R/mkinmod.R117
-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/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
17 files changed, 304 insertions, 143 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/R/mkinmod.R b/R/mkinmod.R
index a1ae0021..cf618525 100644
--- a/R/mkinmod.R
+++ b/R/mkinmod.R
@@ -364,79 +364,76 @@ mkinmod <- function(..., use_of_ff = "min", speclist = NULL, quiet = FALSE, verb
model$coefmat <- m
}#}}}
- # Try to create a function compiled from C code if more than one observed {{{
- # variable and gcc is available
+ # Try to create a function compiled from C code if >1 observed variable {{{
if (length(obs_vars) > 1) {
- if (Sys.which("gcc") != "") {
- # Translate the R code for the derivatives to C code
- diffs.C <- paste(diffs, collapse = ";\n")
- diffs.C <- paste0(diffs.C, ";")
+ # Translate the R code for the derivatives to C code
+ diffs.C <- paste(diffs, collapse = ";\n")
+ diffs.C <- paste0(diffs.C, ";")
- # HS
- diffs.C <- gsub(HS_decline, "(time <= tb ? k1 : k2)", diffs.C, fixed = TRUE)
+ # HS
+ diffs.C <- gsub(HS_decline, "(time <= tb ? k1 : k2)", diffs.C, fixed = TRUE)
- for (i in seq_along(diffs)) {
- state_var <- names(diffs)[i]
+ for (i in seq_along(diffs)) {
+ state_var <- names(diffs)[i]
- # IORE
- if (state_var %in% obs_vars) {
- if (spec[[state_var]]$type == "IORE") {
- diffs.C <- gsub(paste0(state_var, "^N_", state_var),
- paste0("pow(y[", i - 1, "], N_", state_var, ")"),
- diffs.C, fixed = TRUE)
- }
+ # IORE
+ if (state_var %in% obs_vars) {
+ if (spec[[state_var]]$type == "IORE") {
+ diffs.C <- gsub(paste0(state_var, "^N_", state_var),
+ paste0("pow(y[", i - 1, "], N_", state_var, ")"),
+ diffs.C, fixed = TRUE)
}
+ }
- # Replace d_... terms by f[i-1]
- # First line
- pattern <- paste0("^d_", state_var)
- replacement <- paste0("\nf[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
- # Other lines
- pattern <- paste0("\\nd_", state_var)
- replacement <- paste0("\nf[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
+ # Replace d_... terms by f[i-1]
+ # First line
+ pattern <- paste0("^d_", state_var)
+ replacement <- paste0("\nf[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+ # Other lines
+ pattern <- paste0("\\nd_", state_var)
+ replacement <- paste0("\nf[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
- # Replace names of observed variables by y[i],
- # making the implicit assumption that the observed variables only occur after "* "
- pattern <- paste0("\\* ", state_var)
- replacement <- paste0("* y[", i - 1, "]")
- diffs.C <- gsub(pattern, replacement, diffs.C)
- }
+ # Replace names of observed variables by y[i],
+ # making the implicit assumption that the observed variables only occur after "* "
+ pattern <- paste0("\\* ", state_var)
+ replacement <- paste0("* y[", i - 1, "]")
+ diffs.C <- gsub(pattern, replacement, diffs.C)
+ }
- derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric",
- f = "numeric", rpar = "numeric", ipar = "integer")
+ derivs_sig <- signature(n = "integer", t = "numeric", y = "numeric",
+ f = "numeric", rpar = "numeric", ipar = "integer")
- # Declare the time variable in the body of the function if it is used
- derivs_code <- if (spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {
- paste0("double time = *t;\n", diffs.C)
- } else {
- diffs.C
- }
+ # Declare the time variable in the body of the function if it is used
+ derivs_code <- if (spec[[1]]$type %in% c("FOMC", "DFOP", "HS")) {
+ paste0("double time = *t;\n", diffs.C)
+ } else {
+ diffs.C
+ }
- # Define the function initializing the parameters
- npar <- length(parms)
- initpar_code <- paste0(
- "static double parms [", npar, "];\n",
- paste0("#define ", parms, " parms[", 0:(npar - 1), "]\n", collapse = ""),
- "\n",
- "void initpar(void (* odeparms)(int *, double *)) {\n",
- " int N = ", npar, ";\n",
- " odeparms(&N, parms);\n",
- "}\n\n")
+ # Define the function initializing the parameters
+ npar <- length(parms)
+ initpar_code <- paste0(
+ "static double parms [", npar, "];\n",
+ paste0("#define ", parms, " parms[", 0:(npar - 1), "]\n", collapse = ""),
+ "\n",
+ "void initpar(void (* odeparms)(int *, double *)) {\n",
+ " int N = ", npar, ";\n",
+ " odeparms(&N, parms);\n",
+ "}\n\n")
- # Try to build a shared library
- cf <- try(cfunction(list(func = derivs_sig), derivs_code,
- otherdefs = initpar_code,
- verbose = verbose,
- convention = ".C", language = "C"),
- silent = TRUE)
+ # Try to build a shared library
+ cf <- try(cfunction(list(func = derivs_sig), derivs_code,
+ otherdefs = initpar_code,
+ verbose = verbose,
+ convention = ".C", language = "C"),
+ silent = TRUE)
- if (!inherits(cf, "try-error")) {
- if (!quiet) message("Successfully compiled differential equation model from auto-generated C code.")
- model$cf <- cf
- }
+ if (!inherits(cf, "try-error")) {
+ if (!quiet) message("Successfully compiled differential equation model from auto-generated C code.")
+ model$cf <- cf
}
}
# }}}
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/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

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