From 43af185533b11327368148a44e9295ea3eb3abb1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 23 Nov 2023 06:17:28 +0100 Subject: Bump version, fix test from last commit, check and test --- man/hierarchical_kinetics.Rd | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'man') 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 -- cgit v1.2.1 From b07f9fcb7468ac1b5fab0924328fba36ae943be5 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sun, 26 Nov 2023 20:38:30 +0100 Subject: Deal with 'saem' fits failing when updating an 'mhmkin' object --- man/check_failed.Rd | 14 ++++++++++++++ 1 file changed, 14 insertions(+) create mode 100644 man/check_failed.Rd (limited to 'man') 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 +} -- cgit v1.2.1 From e5aea600fd957955fc3e8e41dbc93bf4f65af803 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Thu, 19 Dec 2024 10:59:44 +0100 Subject: Support observed data as tibble Closes #14 --- man/mkinfit.Rd | 3 ++- man/mkinpredict.Rd | 4 ++-- 2 files changed, 4 insertions(+), 3 deletions(-) (limited to 'man') 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..4db4d62f 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 \link[deSolve:ode]{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 \link[deSolve:ode]{deSolve::ode} returns NaN values} } \value{ A matrix with the numeric solution in wide format -- cgit v1.2.1 From 5c54f39802ec2898cd36916ae09e7873a9e95239 Mon Sep 17 00:00:00 2001 From: Ranke Johannes Date: Thu, 19 Dec 2024 15:08:11 +0100 Subject: Skip small symbols in plot.mixed() --- man/plot.mixed.mmkin.Rd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'man') 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, -- cgit v1.2.1 From 328d1173db2395c1a5705b5f0980e2956db8be1f Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 12:43:29 +0100 Subject: Update wordlist, bump date and simplify DESCRIPTION Also, the R-Universe URL that the badge points to is updated --- man/mkinpredict.Rd | 4 ++-- man/nlme.Rd | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) (limited to 'man') 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/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 -- cgit v1.2.1 From 53391cdce906364ace5dfeb1380716425c60ee04 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 14:50:06 +0100 Subject: Update docs --- man/mkinpredict.Rd | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) (limited to 'man') diff --git a/man/mkinpredict.Rd b/man/mkinpredict.Rd index a4821705..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[deSolve:ode]{deSolve::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.} @@ -86,11 +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.} -<<<<<<< HEAD -\item{na_stop}{Should it be an error if \link[deSolve:ode]{deSolve::ode} returns NaN values} -======= \item{na_stop}{Should it be an error if \code{deSolve::ode()} returns NaN values} ->>>>>>> devel } \value{ A matrix with the numeric solution in wide format -- cgit v1.2.1 From 6476f5f49b373cd4cf05f2e73389df83e437d597 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 13 Feb 2025 16:30:31 +0100 Subject: Axis legend formatting, update vignettes --- man/multistart.Rd | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'man') 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) } } -- cgit v1.2.1