diff options
| -rw-r--r-- | .travis.yml | 2 | ||||
| -rw-r--r-- | R/nlme.R | 67 | ||||
| -rw-r--r-- | docs/404.html | 2 | ||||
| -rw-r--r-- | docs/articles/index.html | 2 | ||||
| -rw-r--r-- | docs/authors.html | 2 | ||||
| -rw-r--r-- | docs/index.html | 2 | ||||
| -rw-r--r-- | docs/news/index.html | 2 | ||||
| -rw-r--r-- | docs/reference/endpoints.html | 2 | ||||
| -rw-r--r-- | docs/reference/index.html | 4 | ||||
| -rw-r--r-- | docs/reference/mkinds.html | 2 | ||||
| -rw-r--r-- | docs/reference/mmkin.html | 14 | ||||
| -rw-r--r-- | docs/reference/nlme.html | 114 | ||||
| -rw-r--r-- | docs/reference/plot.mmkin.html | 2 | ||||
| -rw-r--r-- | docs/reference/print.mkinds.html | 2 | ||||
| -rw-r--r-- | man/nlme.Rd | 18 |
15 files changed, 162 insertions, 75 deletions
diff --git a/.travis.yml b/.travis.yml index 172d0236..0d180f7e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -7,7 +7,7 @@ addons: apt: packages: - gcc -github_packages: +r_github_packages: - r-lib/covr script: - | @@ -1,14 +1,12 @@ #' Estimation of parameter distributions from mmkin row objects #' -#' This function sets up and attempts to fit a mixed effects model to +#' These functions facilitate setting up a nonlinear mixed effects model for #' an mmkin row object. 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. #' #' @param object An mmkin row object containing several fits of the same model to different datasets #' @import nlme -#' @importFrom purrr map_dfr -#' @return A named vector containing mean values of the fitted degradation model parameters #' @rdname nlme #' @examples #' sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) @@ -45,7 +43,7 @@ #' summary(m_nlme) #' #' \dontrun{ -#' Test on some real data +#' # Test on some real data #' ds_2 <- lapply(experimental_data_for_UBA_2019[6:10], #' function(x) x$data[c("name", "time", "value")]) #' m_sfo_sfo <- mkinmod(parent = mkinsub("SFO", "A1"), @@ -113,36 +111,7 @@ #' #' anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo) #' } -#' @export -mean_degparms <- function(object) { - if (nrow(object) > 1) stop("Only row objects allowed") - p_mat_start_trans <- sapply(object, parms, transformed = TRUE) - mean_degparm_names <- setdiff(rownames(p_mat_start_trans), names(object[[1]]$errparms)) - res <- apply(p_mat_start_trans[mean_degparm_names, ], 1, mean) - return(res) -} - -#' @rdname nlme -#' @importFrom purrr map_dfr -#' @return A groupedData data object -#' @export -nlme_data <- function(object) { - if (nrow(object) > 1) stop("Only row objects allowed") - ds_names <- colnames(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$variable) - ds_nlme_renamed <- data.frame(ds = ds_nlme$ds, name = ds_nlme$variable, - time = ds_nlme$time, value = ds_nlme$observed, - stringsAsFactors = FALSE) - ds_nlme_grouped <- groupedData(value ~ time | ds, ds_nlme_renamed) - return(ds_nlme_grouped) -} - -#' @rdname nlme -#' @return A function that can be used with nlme +#' @return A function that can be used with \code{link{nlme}} #' @export nlme_function <- function(object) { if (nrow(object) > 1) stop("Only row objects allowed") @@ -211,3 +180,33 @@ nlme_function <- function(object) { model_function <- as.function(c(model_function_alist, model_function_body)) return(model_function) } + +#' @rdname nlme +#' @return A named vector containing mean values of the fitted degradation model parameters +#' @export +mean_degparms <- function(object) { + if (nrow(object) > 1) stop("Only row objects allowed") + degparm_mat_trans <- sapply(object, parms, transformed = TRUE) + mean_degparm_names <- setdiff(rownames(degparm_mat_trans), names(object[[1]]$errparms)) + res <- apply(degparm_mat_trans[mean_degparm_names, ], 1, mean) + return(res) +} + +#' @rdname nlme +#' @importFrom purrr map_dfr +#' @return A \code{\link{groupedData}} object +#' @export +nlme_data <- function(object) { + if (nrow(object) > 1) stop("Only row objects allowed") + ds_names <- colnames(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$variable) + ds_nlme_renamed <- data.frame(ds = ds_nlme$ds, name = ds_nlme$variable, + time = ds_nlme$time, value = ds_nlme$observed, + stringsAsFactors = FALSE) + ds_nlme_grouped <- groupedData(value ~ time | ds, ds_nlme_renamed) + return(ds_nlme_grouped) +} diff --git a/docs/404.html b/docs/404.html index 3658a137..dc3c3c18 100644 --- a/docs/404.html +++ b/docs/404.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/articles/index.html b/docs/articles/index.html index 3e181a2c..4a5087df 100644 --- a/docs/articles/index.html +++ b/docs/articles/index.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/authors.html b/docs/authors.html index 2bb2557a..20c040f9 100644 --- a/docs/authors.html +++ b/docs/authors.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/index.html b/docs/index.html index fe334eb8..7cf11e5c 100644 --- a/docs/index.html +++ b/docs/index.html @@ -37,7 +37,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/news/index.html b/docs/news/index.html index cb5e6df3..c8d7ce3d 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index f201294d..68af5fcf 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -75,7 +75,7 @@ advantage that the SFORB model can also be used for metabolites." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/reference/index.html b/docs/reference/index.html index a3547e29..31f7678c 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -67,7 +67,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> @@ -273,7 +273,7 @@ of an mmkin object</p></td> </tr><tr> <td> - <p><code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> <code><a href="nlme.html">nlme_function()</a></code> </p> + <p><code><a href="nlme.html">nlme_function()</a></code> <code><a href="nlme.html">mean_degparms()</a></code> <code><a href="nlme.html">nlme_data()</a></code> </p> </td> <td><p>Estimation of parameter distributions from mmkin row objects</p></td> </tr> diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index ef6fb35c..946d40a6 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -72,7 +72,7 @@ provided by this package come as mkinds objects nevertheless." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 8e1ea54f..c1f62be7 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -72,7 +72,7 @@ datasets specified in its first two arguments." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> @@ -183,8 +183,9 @@ for parallel execution.</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A matrix of <code><a href='mkinfit.html'>mkinfit</a></code> objects that can be indexed using - the model and dataset names as row and column indices.</p> + <p>A two-dimensional <code><a href='https://rdrr.io/r/base/array.html'>array</a></code> of <code><a href='mkinfit.html'>mkinfit</a></code> + objects that can be indexed using the model names for the first index (row index) + and the dataset names for the second index (column index).</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> <div class='dont-index'><p><code><a href='Extract.mmkin.html'>[.mmkin</a></code> for subsetting, <code><a href='plot.mmkin.html'>plot.mmkin</a></code> for @@ -207,15 +208,12 @@ for parallel execution.</p></td> <span class='no'>time_1</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/system.time.html'>system.time</a></span>(<span class='no'>fits.4</span> <span class='kw'><-</span> <span class='fu'>mmkin</span>(<span class='no'>models</span>, <span class='no'>datasets</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>)) <span class='no'>time_default</span></div><div class='output co'>#> User System verstrichen -#> 18.739 0.379 6.198 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen -#> 19.910 0.000 19.925 </div><div class='input'> +#> 16.471 0.352 5.654 </div><div class='input'><span class='no'>time_1</span></div><div class='output co'>#> User System verstrichen +#> 19.578 0.000 19.590 </div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span>(<span class='no'>fits.0</span><span class='kw'>[[</span><span class='st'>"SFO_lin"</span>, <span class='fl'>2</span>]])</div><div class='output co'>#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 #> -#> $SFORB -#> logical(0) -#> #> $distimes #> DT50 DT90 #> parent 0.8777689 2.915885 diff --git a/docs/reference/nlme.html b/docs/reference/nlme.html index b939d1c3..696916a0 100644 --- a/docs/reference/nlme.html +++ b/docs/reference/nlme.html @@ -6,7 +6,7 @@ <meta http-equiv="X-UA-Compatible" content="IE=edge"> <meta name="viewport" content="width=device-width, initial-scale=1.0"> -<title>Estimation of parameter distributions from mmkin row objects — mean_degparms • mkin</title> +<title>Estimation of parameter distributions from mmkin row objects — nlme_function • mkin</title> <!-- jquery --> @@ -35,8 +35,8 @@ -<meta property="og:title" content="Estimation of parameter distributions from mmkin row objects — mean_degparms" /> -<meta property="og:description" content="This function sets up and attempts to fit a mixed effects model to +<meta property="og:title" content="Estimation of parameter distributions from mmkin row objects — nlme_function" /> +<meta property="og:description" content="These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. 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." /> @@ -72,7 +72,7 @@ datasets." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> @@ -136,17 +136,17 @@ datasets." /> </div> <div class="ref-description"> - <p>This function sets up and attempts to fit a mixed effects model to + <p>These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. 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.</p> </div> - <pre class="usage"><span class='fu'>mean_degparms</span>(<span class='no'>object</span>) + <pre class="usage"><span class='fu'>nlme_function</span>(<span class='no'>object</span>) -<span class='fu'>nlme_data</span>(<span class='no'>object</span>) +<span class='fu'>mean_degparms</span>(<span class='no'>object</span>) -<span class='fu'>nlme_function</span>(<span class='no'>object</span>)</pre> +<span class='fu'>nlme_data</span>(<span class='no'>object</span>)</pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -159,12 +159,102 @@ datasets.</p> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>A named vector containing mean values of the fitted degradation model parameters</p> -<p>A groupedData data object</p> -<p>A function that can be used with nlme</p> + <p>A function that can be used with <code>link{nlme}</code></p> +<p>A named vector containing mean values of the fitted degradation model parameters</p> +<p>A <code><a href='https://rdrr.io/pkg/nlme/man/groupedData.html'>groupedData</a></code> object</p> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <pre class="examples"></pre> + <pre class="examples"><div class='input'><span class='no'>sampling_times</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>0</span>, <span class='fl'>1</span>, <span class='fl'>3</span>, <span class='fl'>7</span>, <span class='fl'>14</span>, <span class='fl'>28</span>, <span class='fl'>60</span>, <span class='fl'>90</span>, <span class='fl'>120</span>) +<span class='no'>m_SFO</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>)) +<span class='no'>d_SFO_1</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.1</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>98</span>), <span class='no'>sampling_times</span>) +<span class='no'>d_SFO_1_long</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_1</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) +<span class='no'>d_SFO_2</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.05</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>102</span>), <span class='no'>sampling_times</span>) +<span class='no'>d_SFO_2_long</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_2</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) +<span class='no'>d_SFO_3</span> <span class='kw'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span>(<span class='no'>m_SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>k_parent_sink</span> <span class='kw'>=</span> <span class='fl'>0.02</span>), + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fl'>103</span>), <span class='no'>sampling_times</span>) +<span class='no'>d_SFO_3_long</span> <span class='kw'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span>(<span class='no'>d_SFO_3</span>, <span class='kw'>time</span> <span class='kw'>=</span> <span class='st'>"time"</span>) + +<span class='no'>d1</span> <span class='kw'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_SFO_1</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>3</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='no'>d2</span> <span class='kw'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_SFO_2</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>2</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='no'>d3</span> <span class='kw'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span>(<span class='no'>d_SFO_3</span>, <span class='kw'>function</span>(<span class='no'>value</span>) <span class='fl'>4</span>, <span class='kw'>n</span> <span class='kw'>=</span> <span class='fl'>1</span>) +<span class='no'>ds</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='kw'>d1</span> <span class='kw'>=</span> <span class='no'>d1</span>, <span class='kw'>d2</span> <span class='kw'>=</span> <span class='no'>d2</span>, <span class='kw'>d3</span> <span class='kw'>=</span> <span class='no'>d3</span>) + +<span class='no'>f</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='st'>"SFO"</span>, <span class='no'>ds</span>, <span class='kw'>cores</span> <span class='kw'>=</span> <span class='fl'>1</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>) +<span class='no'>mean_dp</span> <span class='kw'><-</span> <span class='fu'>mean_degparms</span>(<span class='no'>f</span>) +<span class='no'>grouped_data</span> <span class='kw'><-</span> <span class='fu'>nlme_data</span>(<span class='no'>f</span>) +<span class='no'>nlme_f</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f</span>) + +<span class='fu'><a href='https://rdrr.io/r/base/library.html'>library</a></span>(<span class='no'>nlme</span>) +<span class='no'>m_nlme</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f</span>(<span class='no'>name</span>, <span class='no'>time</span>, <span class='no'>parent_0</span>, <span class='no'>log_k_parent_sink</span>), + <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data</span>, + <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> ~ <span class='fl'>1</span>, + <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> ~ <span class='fl'>1</span>), + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f(name, time, parent_0, log_k_parent_sink): konnte Funktion "nlme_f" nicht finden</span></div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span>(<span class='no'>m_nlme</span>)</div><div class='output co'>#> <span class='error'>Error in summary(m_nlme): Objekt 'm_nlme' nicht gefunden</span></div><div class='input'> +<span class='co'># \dontrun{</span> + <span class='co'># Test on some real data</span> + <span class='no'>ds_2</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span>(<span class='no'>experimental_data_for_UBA_2019</span>[<span class='fl'>6</span>:<span class='fl'>10</span>], + <span class='kw'>function</span>(<span class='no'>x</span>) <span class='no'>x</span>$<span class='no'>data</span>[<span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span>)]) + <span class='no'>m_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"min"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>m_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>, <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>), <span class='kw'>use_of_ff</span> <span class='kw'>=</span> <span class='st'>"max"</span>)</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>m_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"FOMC"</span>, <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>m_dfop_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='no'>m_sforb_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(<span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFORB"</span>, <span class='st'>"A1"</span>), + <span class='kw'>A1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#> <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> + <span class='no'>f_2</span> <span class='kw'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span>(<span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span>(<span class='st'>"SFO-SFO"</span> <span class='kw'>=</span> <span class='no'>m_sfo_sfo</span>, + <span class='st'>"SFO-SFO-ff"</span> <span class='kw'>=</span> <span class='no'>m_sfo_sfo_ff</span>, + <span class='st'>"FOMC-SFO"</span> <span class='kw'>=</span> <span class='no'>m_fomc_sfo</span>, + <span class='st'>"DFOP-SFO"</span> <span class='kw'>=</span> <span class='no'>m_dfop_sfo</span>, + <span class='st'>"SFORB-SFO"</span> <span class='kw'>=</span> <span class='no'>m_sforb_sfo</span>), + <span class='no'>ds_2</span>) + + <span class='no'>grouped_data_2</span> <span class='kw'><-</span> <span class='fu'>nlme_data</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ]) + + <span class='no'>mean_dp_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'>mean_degparms</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ]) + <span class='no'>mean_dp_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'>mean_degparms</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ]) + <span class='no'>mean_dp_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'>mean_degparms</span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ]) + <span class='no'>mean_dp_dfop_sfo</span> <span class='kw'><-</span> <span class='fu'>mean_degparms</span>(<span class='no'>f_2</span>[<span class='st'>"DFOP-SFO"</span>, ]) + <span class='no'>mean_dp_sforb_sfo</span> <span class='kw'><-</span> <span class='fu'>mean_degparms</span>(<span class='no'>f_2</span>[<span class='st'>"SFORB-SFO"</span>, ]) + + <span class='no'>nlme_f_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO"</span>, ]) + <span class='no'>nlme_f_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"SFO-SFO-ff"</span>, ]) + <span class='no'>nlme_f_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'>nlme_function</span>(<span class='no'>f_2</span>[<span class='st'>"FOMC-SFO"</span>, ]) + + <span class='co'># Allowing for correlations between random effects leads to non-convergence</span> + <span class='no'>f_nlme_sfo_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>, + <span class='no'>parent_0</span>, <span class='no'>log_k_parent_sink</span>, <span class='no'>log_k_parent_A1</span>, <span class='no'>log_k_A1_sink</span>), + <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, + <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>, + <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent_sink</span> + <span class='no'>log_k_parent_A1</span> + <span class='no'>log_k_A1_sink</span> ~ <span class='fl'>1</span>), + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo(name, time, parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink): konnte Funktion "nlme_f_sfo_sfo" nicht finden</span></div><div class='input'> + <span class='co'># The same model fitted with transformed formation fractions does not converge</span> + <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>, + <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), + <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, + <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, + <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>), + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'> + <span class='co'># It does converge with this version of reduced random effects</span> + <span class='no'>f_nlme_sfo_sfo_ff</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_sfo_sfo_ff</span>(<span class='no'>name</span>, <span class='no'>time</span>, + <span class='no'>parent_0</span>, <span class='no'>log_k_parent</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), + <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, + <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, + <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_k_parent</span> ~ <span class='fl'>1</span>), + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_sfo_sfo_ff</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_sfo_sfo_ff(name, time, parent_0, log_k_parent, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_sfo_sfo_ff" nicht finden</span></div><div class='input'> + <span class='no'>f_nlme_fomc_sfo</span> <span class='kw'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span>(<span class='no'>value</span> ~ <span class='fu'>nlme_f_fomc_sfo</span>(<span class='no'>name</span>, <span class='no'>time</span>, + <span class='no'>parent_0</span>, <span class='no'>log_alpha</span>, <span class='no'>log_beta</span>, <span class='no'>log_k_A1</span>, <span class='no'>f_parent_ilr_1</span>), + <span class='kw'>data</span> <span class='kw'>=</span> <span class='no'>grouped_data_2</span>, + <span class='kw'>fixed</span> <span class='kw'>=</span> <span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>, + <span class='kw'>random</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span>(<span class='no'>parent_0</span> + <span class='no'>log_alpha</span> + <span class='no'>log_beta</span> + <span class='no'>log_k_A1</span> + <span class='no'>f_parent_ilr_1</span> ~ <span class='fl'>1</span>), + <span class='kw'>start</span> <span class='kw'>=</span> <span class='no'>mean_dp_fomc_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in nlme_f_fomc_sfo(name, time, parent_0, log_alpha, log_beta, log_k_A1, f_parent_ilr_1): konnte Funktion "nlme_f_fomc_sfo" nicht finden</span></div><div class='input'> + <span class='co'># DFOP-SFO and SFORB-SFO did not converge with full random effects</span> + + <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span>(<span class='no'>f_nlme_fomc_sfo</span>, <span class='no'>f_nlme_sfo_sfo</span>)</div><div class='output co'>#> <span class='error'>Error in anova(f_nlme_fomc_sfo, f_nlme_sfo_sfo): Objekt 'f_nlme_fomc_sfo' nicht gefunden</span></div><div class='input'># } +</div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="sidebar"> <h2>Contents</h2> diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index be60f228..a513756b 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -73,7 +73,7 @@ the fit of at least one model to the same dataset is shown." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index de1a2410..824d961b 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -69,7 +69,7 @@ </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.9</span> + <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.49.10</span> </span> </div> diff --git a/man/nlme.Rd b/man/nlme.Rd index e74ba16d..7527f09d 100644 --- a/man/nlme.Rd +++ b/man/nlme.Rd @@ -1,29 +1,29 @@ % Generated by roxygen2: do not edit by hand % Please edit documentation in R/nlme.R -\name{mean_degparms} +\name{nlme_function} +\alias{nlme_function} \alias{mean_degparms} \alias{nlme_data} -\alias{nlme_function} \title{Estimation of parameter distributions from mmkin row objects} \usage{ +nlme_function(object) + mean_degparms(object) nlme_data(object) - -nlme_function(object) } \arguments{ \item{object}{An mmkin row object containing several fits of the same model to different datasets} } \value{ -A named vector containing mean values of the fitted degradation model parameters +A function that can be used with \code{link{nlme}} -A groupedData data object +A named vector containing mean values of the fitted degradation model parameters -A function that can be used with nlme +A \code{\link{groupedData}} object } \description{ -This function sets up and attempts to fit a mixed effects model to +These functions facilitate setting up a nonlinear mixed effects model for an mmkin row object. 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. @@ -63,7 +63,7 @@ m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), summary(m_nlme) \dontrun{ - Test on some real data + # Test on some real data 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"), |