diff options
Diffstat (limited to 'man')
| -rw-r--r-- | man/check_failed.Rd | 14 | ||||
| -rw-r--r-- | man/hierarchical_kinetics.Rd | 6 | ||||
| -rw-r--r-- | man/mkinfit.Rd | 3 | ||||
| -rw-r--r-- | man/mkinpredict.Rd | 4 | ||||
| -rw-r--r-- | man/multistart.Rd | 4 | ||||
| -rw-r--r-- | man/nlme.Rd | 2 | ||||
| -rw-r--r-- | man/plot.mixed.mmkin.Rd | 2 |
7 files changed, 27 insertions, 8 deletions
diff --git a/man/check_failed.Rd b/man/check_failed.Rd new file mode 100644 index 00000000..85029024 --- /dev/null +++ b/man/check_failed.Rd @@ -0,0 +1,14 @@ +% Generated by roxygen2: do not edit by hand +% Please edit documentation in R/mhmkin.R +\name{check_failed} +\alias{check_failed} +\title{Check if fit within an mhmkin object failed} +\usage{ +check_failed(x) +} +\arguments{ +\item{x}{The object to be checked} +} +\description{ +Check if fit within an mhmkin object failed +} diff --git a/man/hierarchical_kinetics.Rd b/man/hierarchical_kinetics.Rd index bcbe1e06..8330fe68 100644 --- a/man/hierarchical_kinetics.Rd +++ b/man/hierarchical_kinetics.Rd @@ -9,7 +9,11 @@ hierarchical_kinetics(..., keep_tex = FALSE) \arguments{ \item{...}{Arguments to \code{rmarkdown::pdf_document}} -\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF} +\item{keep_tex}{Keep the intermediate tex file used in the conversion to PDF. +Note that this argument does not control whether to keep the auxiliary +files (e.g., \file{.aux}) generated by LaTeX when compiling \file{.tex} to +\file{.pdf}. To keep these files, you may set \code{options(tinytex.clean = +FALSE)}.} } \value{ R Markdown output format to pass to diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd index f96b4d22..edec9546 100644 --- a/man/mkinfit.Rd +++ b/man/mkinfit.Rd @@ -39,7 +39,8 @@ model to be fitted to the data, or one of the shorthand names ("SFO", parent only degradation model is generated for the variable with the highest value in \code{observed}.} -\item{observed}{A dataframe with the observed data. The first column called +\item{observed}{A dataframe or an object coercible to a dataframe +(e.g. a \code{tibble}) with the observed data. The first column called "name" must contain the name of the observed variable for each data point. The second column must contain the times of observation, named "time". The third column must be named "value" and contain the observed values. diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd index 792d0e47..f68f6c7a 100644 --- a/man/mkinpredict.Rd +++ b/man/mkinpredict.Rd @@ -71,7 +71,7 @@ parent compound.} \item{use_symbols}{If set to \code{TRUE} (default), symbol info present in the \link{mkinmod} object is used if available for accessing compiled code} -\item{method.ode}{The solution method passed via \link{mkinpredict} to \link{ode}] in +\item{method.ode}{The solution method passed via \link{mkinpredict} to \code{deSolve::ode()} in case the solution type is "deSolve" and we are not using compiled code. When using compiled code, only lsoda is supported.} @@ -86,7 +86,7 @@ the observed variables (default) or for all state variables (if set to FALSE). Setting this to FALSE has no effect for analytical solutions, as these always return mapped output.} -\item{na_stop}{Should it be an error if \link{ode} returns NaN values} +\item{na_stop}{Should it be an error if \code{deSolve::ode()} returns NaN values} } \value{ A matrix with the numeric solution in wide format diff --git a/man/multistart.Rd b/man/multistart.Rd index 0df29bfa..d3c23bcf 100644 --- a/man/multistart.Rd +++ b/man/multistart.Rd @@ -77,7 +77,7 @@ dmta_ds[["Elliot 1"]] <- dmta_ds[["Elliot 2"]] <- NULL f_mmkin <- mmkin("DFOP", dmta_ds, error_model = "tc", cores = 7, quiet = TRUE) f_saem_full <- saem(f_mmkin) f_saem_full_multi <- multistart(f_saem_full, n = 16, cores = 16) -parplot(f_saem_full_multi, lpos = "topleft") +parplot(f_saem_full_multi, lpos = "topleft", las = 2) illparms(f_saem_full) f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") @@ -87,7 +87,7 @@ illparms(f_saem_reduced) library(parallel) cl <- makePSOCKcluster(12) f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cluster = cl) -parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2)) +parplot(f_saem_reduced_multi, lpos = "topright", ylim = c(0.5, 2), las = 2) stopCluster(cl) } } diff --git a/man/nlme.Rd b/man/nlme.Rd index e87b7a00..2c92f31b 100644 --- a/man/nlme.Rd +++ b/man/nlme.Rd @@ -15,7 +15,7 @@ nlme_data(object) \value{ A function that can be used with nlme -A \code{\link{groupedData}} object +A \code{nlme::groupedData} object } \description{ These functions facilitate setting up a nonlinear mixed effects model for diff --git a/man/plot.mixed.mmkin.Rd b/man/plot.mixed.mmkin.Rd index 1e264db3..3c44510d 100644 --- a/man/plot.mixed.mmkin.Rd +++ b/man/plot.mixed.mmkin.Rd @@ -25,7 +25,7 @@ nrow.legend = ceiling((length(i) + 1)/ncol.legend), rel.height.legend = 0.02 + 0.07 * nrow.legend, rel.height.bottom = 1.1, - pch_ds = 1:length(i), + pch_ds = c(1:25, 33, 35:38, 40:41, 47:57, 60:90)[1:length(i)], col_ds = pch_ds + 1, lty_ds = col_ds, frame = TRUE, |