diff options
25 files changed, 450 insertions, 213 deletions
@@ -16,11 +16,10 @@ S3method(nlme,mmkin) S3method(nobs,mkinfit) S3method(parms,mkinfit) S3method(parms,mmkin) +S3method(plot,mixed.mmkin) S3method(plot,mkinfit) S3method(plot,mmkin) S3method(plot,nafta) -S3method(plot,nlme.mmkin) -S3method(plot,saem.mmkin) S3method(print,mkinds) S3method(print,mkinmod) S3method(print,mmkin) @@ -1,6 +1,8 @@ # mkin 0.9.50.4 (unreleased) -- 'saem' generic function to fit saemix models, with a method 'saem.mmkin' and a corresponding 'summary.saem.mmkin' +- 'plot.mixed.mmkin' method used for 'nlme.mmkin' and 'saem.mmkin', both inheriting from 'mixed.mmkin' (currently virtual) + +- 'saem' generic function to fit saemix models, with a generator 'saem.mmkin', summary and plot methods - 'transform_odeparms', 'backtransform_odeparms': Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R index 695c63e9..8d875fee 100644 --- a/R/nlme.mmkin.R +++ b/R/nlme.mmkin.R @@ -43,13 +43,14 @@ get_deg_func <- function() { #' @param control passed to nlme #' @param verbose passed to nlme #' @importFrom stats na.fail as.formula -#' @return Upon success, a fitted nlme.mmkin object, which is an nlme object -#' with additional elements +#' @return Upon success, a fitted 'nlme.mmkin' object, which is an nlme object +#' with additional elements. It also inherits from 'mixed.mmkin'. #' @note As the object inherits from [nlme::nlme], there is a wealth of #' methods that will automatically work on 'nlme.mmkin' objects, such as #' [nlme::intervals()], [nlme::anova.lme()] and [nlme::coef.lme()]. #' @export -#' @seealso [nlme_function()] +#' @seealso [nlme_function()], [plot.mixed.mmkin], [summary.nlme.mmkin], +#' [parms.nlme.mmkin] #' @examples #' ds <- lapply(experimental_data_for_UBA_2019[6:10], #' function(x) subset(x$data[c("name", "time", "value")], name == "parent")) @@ -203,7 +204,7 @@ nlme.mmkin <- function(model, data = sys.frame(sys.parent()), val$nlmeversion <- as.character(utils::packageVersion("nlme")) val$mkinversion <- as.character(utils::packageVersion("mkin")) val$Rversion <- paste(R.version$major, R.version$minor, sep=".") - class(val) <- c("nlme.mmkin", "nlme", "lme") + class(val) <- c("nlme.mmkin", "mixed.mmkin", "nlme", "lme") return(val) } diff --git a/R/plot_mixed.R b/R/plot.mixed.mmkin.R index 68404de4..903c3213 100644 --- a/R/plot_mixed.R +++ b/R/plot.mixed.mmkin.R @@ -2,7 +2,6 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object #' -#' @name plot_mixed #' @param x An object of class [saem.mmkin] or [nlme.mmkin] #' @param i A numeric index to select datasets for which to plot the individual predictions, #' in case plots get too large @@ -21,7 +20,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' @param pch_ds Symbols to be used for plotting the data. #' @param lty_ds Line types to be used for the model predictions. #' @importFrom stats coefficients -#' @return The functions are called for their side effect. +#' @return The function is called for its side effect. #' @author Johannes Ranke #' @examples #' ds <- lapply(experimental_data_for_UBA_2019[6:10], @@ -33,7 +32,6 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) #' plot(f[, 3:4], standardized = TRUE) #' -#' library(nlme) #' # For this fit we need to increase pnlsMaxiter, and we increase the #' # tolerance in order to speed up the fit for this example evaluation #' f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) @@ -42,9 +40,9 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' f_saem <- saem(f) #' plot(f_saem) #' } -#' @rdname plot_mixed #' @export -plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin), +plot.mixed.mmkin <- function(x, + i = 1:ncol(x$mmkin), obs_vars = names(x$mkinmod$map), standardized = TRUE, xlab = "Time", @@ -58,89 +56,30 @@ plot.saem.mmkin <- function(x, i = 1:ncol(x$mmkin), pch_ds = 1:length(i), col_ds = pch_ds + 1, lty_ds = col_ds, - frame = TRUE, ...) + frame = TRUE, ... +) { + # Prepare parameters and data fit_1 <- x$mmkin[[1]] ds_names <- colnames(x$mmkin) - degparms_optim <- saemix::psi(x$so) - rownames(degparms_optim) <- ds_names - degparms_optim_names <- setdiff(names(fit_1$par), names(fit_1$errparms)) - colnames(degparms_optim) <- degparms_optim_names - - residual_type = ifelse(standardized, "iwres", "ires") - - residuals <- x$so@results@predictions[[residual_type]] - - degparms_pop <- x$so@results@fixed.effects - names(degparms_pop) <- degparms_optim_names - - .plot_mixed(x, i, - degparms_optim, degparms_pop, residuals, - obs_vars, standardized, xlab, xlim, - resplot, ymax, maxabs, - ncol.legend, nrow.legend, - rel.height.legend, rel.height.bottom, - pch_ds, col_ds, lty_ds, frame, ...) -} - -#' @rdname plot_mixed -#' @export -plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin), - obs_vars = names(x$mkinmod$map), - standardized = TRUE, - xlab = "Time", - xlim = range(x$data$time), - resplot = c("predicted", "time"), - ymax = "auto", maxabs = "auto", - ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), - nrow.legend = ceiling((length(i) + 1) / ncol.legend), - rel.height.legend = 0.03 + 0.08 * nrow.legend, - rel.height.bottom = 1.1, - pch_ds = 1:length(i), - col_ds = pch_ds + 1, - lty_ds = col_ds, - frame = TRUE, ...) -{ - degparms_optim <- coefficients(x) - degparms_pop <- nlme::fixef(x) - - residuals <- residuals(x, - type = ifelse(standardized, "pearson", "response")) - - .plot_mixed(x, i, - degparms_optim, degparms_pop, residuals, - obs_vars, standardized, xlab, xlim, - resplot, ymax, maxabs, - ncol.legend, nrow.legend, - rel.height.legend, rel.height.bottom, - pch_ds, col_ds, lty_ds, frame, ...) -} - -.plot_mixed <- function(x, i = 1:ncol(x$mmkin), - degparms_optim, - degparms_pop, - residuals, - obs_vars = names(x$mkinmod$map), - standardized = TRUE, - xlab = "Time", - xlim = range(x$data$time), - resplot = c("predicted", "time"), - ymax = "auto", maxabs = "auto", - ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), - nrow.legend = ceiling((length(i) + 1) / ncol.legend), - rel.height.legend = 0.03 + 0.08 * nrow.legend, - rel.height.bottom = 1.1, - pch_ds = 1:length(i), - col_ds = pch_ds + 1, - lty_ds = col_ds, - frame = TRUE, ...) -{ - - oldpar <- par(no.readonly = TRUE) + if (inherits(x, "nlme.mmkin")) { + degparms_optim <- coefficients(x) + degparms_pop <- nlme::fixef(x) + residuals <- residuals(x, + type = ifelse(standardized, "pearson", "response")) + } - fit_1 <- x$mmkin[[1]] - ds_names <- colnames(x$mmkin) + if (inherits(x, "saem.mmkin")) { + degparms_optim <- saemix::psi(x$so) + rownames(degparms_optim) <- ds_names + degparms_optim_names <- setdiff(names(fit_1$par), names(fit_1$errparms)) + colnames(degparms_optim) <- degparms_optim_names + residual_type = ifelse(standardized, "iwres", "ires") + residuals <- x$so@results@predictions[[residual_type]] + degparms_pop <- x$so@results@fixed.effects + names(degparms_pop) <- degparms_optim_names + } degparms_fixed <- fit_1$fixed$value names(degparms_fixed) <- rownames(fit_1$fixed) @@ -161,29 +100,6 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin), observed <- cbind(x$data, residual = residuals) - n_plot_rows = length(obs_vars) - n_plots = n_plot_rows * 2 - - # Set relative plot heights, so the first plot row is the norm - rel.heights <- if (n_plot_rows > 1) { - c(rel.height.legend, c(rep(1, n_plot_rows - 1), rel.height.bottom)) - } else { - c(rel.height.legend, 1) - } - - layout_matrix = matrix(c(1, 1, 2:(n_plots + 1)), - n_plot_rows + 1, 2, byrow = TRUE) - layout(layout_matrix, heights = rel.heights) - - par(mar = c(0.1, 2.1, 0.6, 2.1)) - - plot(0, type = "n", axes = FALSE, ann = FALSE) - legend("center", bty = "n", ncol = ncol.legend, - legend = c("Population", ds_names[i]), - lty = c(1, lty_ds), lwd = c(2, rep(1, length(i))), - col = c(1, col_ds), - pch = c(NA, pch_ds)) - solution_type = fit_1$solution_type outtimes <- sort(unique(c(x$data$time, @@ -220,6 +136,32 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin), outtimes, solution_type = solution_type, atol = fit_1$atol, rtol = fit_1$rtol)) + # Start of graphical section + oldpar <- par(no.readonly = TRUE) + + n_plot_rows = length(obs_vars) + n_plots = n_plot_rows * 2 + + # Set relative plot heights, so the first plot row is the norm + rel.heights <- if (n_plot_rows > 1) { + c(rel.height.legend, c(rep(1, n_plot_rows - 1), rel.height.bottom)) + } else { + c(rel.height.legend, 1) + } + + layout_matrix = matrix(c(1, 1, 2:(n_plots + 1)), + n_plot_rows + 1, 2, byrow = TRUE) + layout(layout_matrix, heights = rel.heights) + + par(mar = c(0.1, 2.1, 0.6, 2.1)) + + plot(0, type = "n", axes = FALSE, ann = FALSE) + legend("center", bty = "n", ncol = ncol.legend, + legend = c("Population", ds_names[i]), + lty = c(1, lty_ds), lwd = c(2, rep(1, length(i))), + col = c(1, col_ds), + pch = c(NA, pch_ds)) + resplot <- match.arg(resplot) # Loop plot rows @@ -24,8 +24,9 @@ #' @param \dots Further parameters passed to [saemix::saemixData] #' and [saemix::saemixModel]. #' @return An S3 object of class 'saem.mmkin', containing the fitted -#' [saemix::SaemixObject] as a list component named 'so'. -#' @seealso [summary.saem.mmkin] +#' [saemix::SaemixObject] as a list component named 'so'. The +#' object also inherits from 'mixed.mmkin'. +#' @seealso [summary.saem.mmkin] [plot.mixed.mmkin] #' @examples #' \dontrun{ #' ds <- lapply(experimental_data_for_UBA_2019[6:10], @@ -134,7 +135,7 @@ saem.mmkin <- function(object, Rversion = paste(R.version$major, R.version$minor, sep=".") ) - class(result) <- "saem.mmkin" + class(result) <- c("saem.mmkin", "mixed.mmkin") return(result) } diff --git a/_pkgdown.yml b/_pkgdown.yml index 61c69a9d..75296568 100644 --- a/_pkgdown.yml +++ b/_pkgdown.yml @@ -42,11 +42,10 @@ reference: desc: Create and work with nonlinear mixed effects models contents: - nlme.mmkin - - plot.nlme.mmkin - - summary.nlme.mmkin - saem.mmkin + - plot.mixed.mmkin + - summary.nlme.mmkin - summary.saem.mmkin - - plot.saem.mmkin - nlme_function - get_deg_func - saemix_model diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index 4f811b9f..c068b8a4 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -146,7 +146,7 @@ <a href="#mkin-0-9-50-4-unreleased" class="anchor"></a>mkin 0.9.50.4 (unreleased)<small> Unreleased </small> </h1> <ul> -<li><p>‘saem’ generic function to fit saemix models, with a method ‘saem.mmkin’ and a corresponding ‘summary.saem.mmkin’</p></li> +<li><p>‘saem’ generic function to fit saemix models, with a generator ‘saem.mmkin’ and further methods ‘summary.saem.mmkin’, ‘plot.saem.mmkin’</p></li> <li><p>‘transform_odeparms’, ‘backtransform_odeparms’: Use logit transformation for solitary fractions like the g parameter of the DFOP model, or formation fractions for a pathway to only one target variable</p></li> <li><p>‘update’ method for ‘mmkin’ objects</p></li> <li><p>‘plot’, ‘summary’ and ‘print’ methods for ‘nlme.mmkin’ objects</p></li> diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 4b2b76f7..ef9bb681 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -10,7 +10,7 @@ articles: web_only/NAFTA_examples: NAFTA_examples.html web_only/benchmarks: benchmarks.html web_only/compiled_models: compiled_models.html -last_built: 2020-11-09T15:29Z +last_built: 2020-11-09T16:21Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png Binary files differindex cfc5bc2b..fc26276a 100644 --- a/docs/dev/reference/Rplot001.png +++ b/docs/dev/reference/Rplot001.png diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png Binary files differindex 8ada7133..48e8698c 100644 --- a/docs/dev/reference/Rplot002.png +++ b/docs/dev/reference/Rplot002.png diff --git a/docs/dev/reference/Rplot003.png b/docs/dev/reference/Rplot003.png Binary files differindex cd2014eb..b4581e35 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/index.html b/docs/dev/reference/index.html index 5ed2044b..ada9fb24 100644 --- a/docs/dev/reference/index.html +++ b/docs/dev/reference/index.html @@ -325,21 +325,21 @@ of an mmkin object</p></td> </tr><tr> <td> - <p><code><a href="plot_mixed.html">plot(<i><saem.mmkin></i>)</a></code> <code><a href="plot_mixed.html">plot(<i><nlme.mmkin></i>)</a></code> </p> + <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p> </td> - <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td> + <td><p>Fit nonlinear mixed models with SAEM</p></td> </tr><tr> <td> - <p><code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> </p> + <p><code><a href="plot.mixed.mmkin.html">plot(<i><mixed.mmkin></i>)</a></code> </p> </td> - <td><p>Summary method for class "nlme.mmkin"</p></td> + <td><p>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object</p></td> </tr><tr> <td> - <p><code><a href="saem.html">saem()</a></code> <code><a href="saem.html">saemix_model()</a></code> <code><a href="saem.html">saemix_data()</a></code> </p> + <p><code><a href="summary.nlme.mmkin.html">summary(<i><nlme.mmkin></i>)</a></code> <code><a href="summary.nlme.mmkin.html">print(<i><summary.nlme.mmkin></i>)</a></code> </p> </td> - <td><p>Fit nonlinear mixed models with SAEM</p></td> + <td><p>Summary method for class "nlme.mmkin"</p></td> </tr><tr> <td> diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png Binary files differindex 04d8b234..25bebeca 100644 --- a/docs/dev/reference/nlme.mmkin-1.png +++ b/docs/dev/reference/nlme.mmkin-1.png diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png Binary files differindex 281d6024..46846067 100644 --- a/docs/dev/reference/nlme.mmkin-3.png +++ b/docs/dev/reference/nlme.mmkin-3.png diff --git a/docs/dev/reference/nlme.mmkin-4.png b/docs/dev/reference/nlme.mmkin-4.png Binary files differindex d504e8f0..6724163f 100644 --- a/docs/dev/reference/nlme.mmkin-4.png +++ b/docs/dev/reference/nlme.mmkin-4.png diff --git a/docs/dev/reference/nlme.mmkin.html b/docs/dev/reference/nlme.mmkin.html index c3cc53ff..defef75d 100644 --- a/docs/dev/reference/nlme.mmkin.html +++ b/docs/dev/reference/nlme.mmkin.html @@ -152,7 +152,7 @@ have been obtained by fitting the same model to a list of datasets.</p> </div> <pre class="usage"><span class='co'># S3 method for mmkin</span> -<span class='fu'>nlme</span><span class='op'>(</span> +<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span> <span class='va'>model</span>, data <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.frame</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/sys.parent.html'>sys.parent</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span>, <span class='va'>fixed</span>, @@ -253,8 +253,8 @@ parameters taken from the mmkin object are used</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> - <p>Upon success, a fitted nlme.mmkin object, which is an nlme object -with additional elements</p> + <p>Upon success, a fitted 'nlme.mmkin' object, which is an nlme object +with additional elements. It also inherits from 'mixed.mmkin'.</p> <h2 class="hasAnchor" id="note"><a class="anchor" href="#note"></a>Note</h2> <p>As the object inherits from <a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme::nlme</a>, there is a wealth of @@ -262,7 +262,8 @@ methods that will automatically work on 'nlme.mmkin' objects, such as <code><a href='https://rdrr.io/pkg/nlme/man/intervals.html'>nlme::intervals()</a></code>, <code><a href='https://rdrr.io/pkg/nlme/man/anova.lme.html'>nlme::anova.lme()</a></code> and <code><a href='https://rdrr.io/pkg/nlme/man/coef.lme.html'>nlme::coef.lme()</a></code>.</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='nlme_function.html'>nlme_function()</a></code></p></div> + <div class='dont-index'><p><code><a href='nlme_function.html'>nlme_function()</a></code>, <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a>, <a href='summary.nlme.mmkin.html'>summary.nlme.mmkin</a>, +parms.nlme.mmkin</p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, @@ -288,21 +289,21 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Log-likelihood: -238.5635 #> #> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) -#> parent_0 log_k1 log_k2 g_ilr -#> 94.17015133 -1.80015306 -4.14738870 0.02290935 +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) +#> parent_0 log_k1 log_k2 g_qlogis +#> 94.17015185 -1.80015278 -4.14738834 0.03239833 #> #> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_ilr Residual -#> StdDev: 2.488249 0.8447273 1.32965 0.3289311 2.321364 +#> parent_0 log_k1 log_k2 g_qlogis Residual +#> StdDev: 2.488249 0.8447275 1.32965 0.4651789 2.321364 #> </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='img'><img src='nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop</span><span class='op'>)</span> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 -#> parent 10.79857 100.7937 30.34193 4.193938 43.85443 +#> parent 10.79857 100.7937 30.34192 4.193937 43.85442 #> </div><div class='input'> <span class='co'># \dontrun{</span> <span class='va'>f_nlme_2</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span>, start <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent_0 <span class='op'>=</span> <span class='fl'>100</span>, log_k_parent <span class='op'>=</span> <span class='fl'>0.1</span><span class='op'>)</span><span class='op'>)</span> @@ -353,35 +354,35 @@ methods that will automatically work on 'nlme.mmkin' objects, such as control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>5e-4</span><span class='op'>)</span>, verbose <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> </div><div class='output co'>#> #> **Iteration 1 -#> LME step: Loglik: -404.9582, nlminb iterations: 1 +#> LME step: Loglik: -404.9583, nlminb iterations: 1 #> reStruct parameters: #> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.4114355 0.9798697 1.6990037 0.7293315 0.3354323 1.7113046 +#> -0.4114356 0.9798646 1.3524300 0.7293315 0.3354323 1.3647313 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3644 -#> fixed effects: 93.82269 -5.455991 -0.6788957 -1.862196 -4.199671 0.05532828 +#> PNLS step: RSS = 630.3633 +#> fixed effects: 93.82269 -5.455993 -0.9601037 -1.862196 -4.199671 0.07824609 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 0.7885368 0.5822683 +#> 0.7897284 0.5822782 #> #> **Iteration 2 #> LME step: Loglik: -407.7755, nlminb iterations: 11 #> reStruct parameters: -#> ds1 ds2 ds3 ds4 ds5 ds6 -#> -0.371224133 0.003056179 1.789939402 0.724671158 0.301602977 1.754200729 +#> ds1 ds2 ds3 ds4 ds5 ds6 +#> -0.37122411 0.00305562 1.44336560 0.72467122 0.30160310 1.40762692 #> Beginning PNLS step: .. completed fit_nlme() step. -#> PNLS step: RSS = 630.3633 -#> fixed effects: 93.82269 -5.455992 -0.6788958 -1.862196 -4.199671 0.05532831 +#> PNLS step: RSS = 630.3637 +#> fixed effects: 93.82269 -5.455992 -0.9601036 -1.862196 -4.199671 0.0782462 #> iterations: 120 #> Convergence crit. (must all become <= tolerance = 0.0005): #> fixed reStruct -#> 4.789774e-07 2.200661e-05 </div><div class='input'> +#> 1.375673e-06 9.758294e-06 </div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span><span class='op'>)</span> </div><div class='img'><img src='nlme.mmkin-4.png' alt='' width='700' height='433' /></div><div class='input'> <span class='fu'><a href='https://rdrr.io/r/stats/anova.html'>anova</a></span><span class='op'>(</span><span class='va'>f_nlme_dfop_sfo</span>, <span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> Model df AIC BIC logLik Test L.Ratio p-value -#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9273 +#> f_nlme_dfop_sfo 1 13 843.8547 884.6201 -408.9274 #> f_nlme_sfo_sfo 2 9 1085.1821 1113.4043 -533.5910 1 vs 2 249.3274 <.0001</div><div class='input'> <span class='fu'><a href='endpoints.html'>endpoints</a></span><span class='op'>(</span><span class='va'>f_nlme_sfo_sfo</span><span class='op'>)</span> </div><div class='output co'>#> $ff @@ -400,7 +401,7 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 11.07091 104.6320 31.49738 4.462384 46.20825 -#> A1 162.30536 539.1667 NA NA NA +#> A1 162.30523 539.1663 NA NA NA #> </div><div class='input'> <span class='kw'>if</span> <span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='fu'>findFunction</span><span class='op'>(</span><span class='st'>"varConstProp"</span><span class='op'>)</span><span class='op'>)</span> <span class='op'>></span> <span class='fl'>0</span><span class='op'>)</span> <span class='op'>{</span> <span class='co'># tc error model for nlme available</span> <span class='co'># Attempts to fit metabolite kinetics with the tc error model are possible,</span> @@ -425,23 +426,23 @@ methods that will automatically work on 'nlme.mmkin' objects, such as #> Log-likelihood: -238.4298 #> #> Fixed effects: -#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) -#> parent_0 log_k1 log_k2 g_ilr -#> 94.04774463 -1.82339924 -4.16715509 0.04020161 +#> list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) +#> parent_0 log_k1 log_k2 g_qlogis +#> 94.04774566 -1.82339808 -4.16715311 0.05685186 #> #> Random effects: -#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_ilr ~ 1) +#> Formula: list(parent_0 ~ 1, log_k1 ~ 1, log_k2 ~ 1, g_qlogis ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k1 log_k2 g_ilr Residual -#> StdDev: 2.473883 0.8499901 1.337187 0.3294411 1 +#> parent_0 log_k1 log_k2 g_qlogis Residual +#> StdDev: 2.473881 0.8499884 1.337185 0.4659005 1 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: #> const prop -#> 2.23222625 0.01262414 </div><div class='input'> +#> 2.23224114 0.01262341 </div><div class='input'> <span class='va'>f_2_obs</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"SFO-SFO"</span> <span class='op'>=</span> <span class='va'>m_sfo_sfo</span>, <span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>m_dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds_2</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span>, error_model <span class='op'>=</span> <span class='st'>"obs"</span><span class='op'>)</span> diff --git a/docs/dev/reference/plot.mixed.mmkin-1.png b/docs/dev/reference/plot.mixed.mmkin-1.png Binary files differnew file mode 100644 index 00000000..5cb33214 --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin-1.png diff --git a/docs/dev/reference/plot.mixed.mmkin-2.png b/docs/dev/reference/plot.mixed.mmkin-2.png Binary files differnew file mode 100644 index 00000000..c0d67204 --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin-2.png diff --git a/docs/dev/reference/plot.mixed.mmkin-3.png b/docs/dev/reference/plot.mixed.mmkin-3.png Binary files differnew file mode 100644 index 00000000..67058e6c --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin-3.png diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html new file mode 100644 index 00000000..4108aea3 --- /dev/null +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -0,0 +1,313 @@ +<!-- Generated by pkgdown: do not edit by hand --> +<!DOCTYPE html> +<html lang="en"> + <head> + <meta charset="utf-8"> +<meta http-equiv="X-UA-Compatible" content="IE=edge"> +<meta name="viewport" content="width=device-width, initial-scale=1.0"> + +<title>Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row 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class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/nrow.html'>ncol</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mmkin</span><span class='op'>)</span>, + obs_vars <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>mkinmod</span><span class='op'>$</span><span class='va'>map</span><span class='op'>)</span>, + standardized <span class='op'>=</span> <span class='cn'>TRUE</span>, + xlab <span class='op'>=</span> <span class='st'>"Time"</span>, + xlim <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/range.html'>range</a></span><span class='op'>(</span><span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>$</span><span class='va'>time</span><span class='op'>)</span>, + resplot <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"predicted"</span>, <span class='st'>"time"</span><span class='op'>)</span>, + ymax <span class='op'>=</span> <span class='st'>"auto"</span>, + maxabs <span class='op'>=</span> <span class='st'>"auto"</span>, + ncol.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'><=</span> <span class='fl'>3</span>, <span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span>, <span class='fu'><a href='https://rdrr.io/r/base/ifelse.html'>ifelse</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'><=</span> <span class='fl'>8</span>, <span class='fl'>3</span>, <span class='fl'>4</span><span class='op'>)</span><span class='op'>)</span>, + nrow.legend <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/Round.html'>ceiling</a></span><span class='op'>(</span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span> <span class='op'>+</span> <span class='fl'>1</span><span class='op'>)</span><span class='op'>/</span><span class='va'>ncol.legend</span><span class='op'>)</span>, + rel.height.legend <span class='op'>=</span> <span class='fl'>0.03</span> <span class='op'>+</span> <span class='fl'>0.08</span> <span class='op'>*</span> <span class='va'>nrow.legend</span>, + rel.height.bottom <span class='op'>=</span> <span class='fl'>1.1</span>, + pch_ds <span class='op'>=</span> <span class='fl'>1</span><span class='op'>:</span><span class='fu'><a href='https://rdrr.io/r/base/length.html'>length</a></span><span class='op'>(</span><span class='va'>i</span><span class='op'>)</span>, + col_ds <span class='op'>=</span> <span class='va'>pch_ds</span> <span class='op'>+</span> <span class='fl'>1</span>, + lty_ds <span class='op'>=</span> <span class='va'>col_ds</span>, + frame <span class='op'>=</span> <span class='cn'>TRUE</span>, + <span class='va'>...</span> +<span class='op'>)</span></pre> + + <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> + <table class="ref-arguments"> + <colgroup><col class="name" /><col class="desc" /></colgroup> + <tr> + <th>x</th> + <td><p>An object of class <a href='saem.html'>saem.mmkin</a> or <a href='nlme.mmkin.html'>nlme.mmkin</a></p></td> + </tr> + <tr> + <th>i</th> + <td><p>A numeric index to select datasets for which to plot the individual predictions, +in case plots get too large</p></td> + </tr> + <tr> + <th>obs_vars</th> + <td><p>A character vector of names of the observed variables for +which the data and the model should be plotted. Defauls to all observed +variables in the model.</p></td> + </tr> + <tr> + <th>standardized</th> + <td><p>Should the residuals be standardized? Only takes effect if +<code>resplot = "time"</code>.</p></td> + </tr> + <tr> + <th>xlab</th> + <td><p>Label for the x axis.</p></td> + </tr> + <tr> + <th>xlim</th> + <td><p>Plot range in x direction.</p></td> + </tr> + <tr> + <th>resplot</th> + <td><p>Should the residuals plotted against time or against +predicted values?</p></td> + </tr> + <tr> + <th>ymax</th> + <td><p>Vector of maximum y axis values</p></td> + </tr> + <tr> + <th>maxabs</th> + <td><p>Maximum absolute value of the residuals. This is used for the +scaling of the y axis and defaults to "auto".</p></td> + </tr> + <tr> + <th>ncol.legend</th> + <td><p>Number of columns to use in the legend</p></td> + </tr> + <tr> + <th>nrow.legend</th> + <td><p>Number of rows to use in the legend</p></td> + </tr> + <tr> + <th>rel.height.legend</th> + <td><p>The relative height of the legend shown on top</p></td> + </tr> + <tr> + <th>rel.height.bottom</th> + <td><p>The relative height of the bottom plot row</p></td> + </tr> + <tr> + <th>pch_ds</th> + <td><p>Symbols to be used for plotting the data.</p></td> + </tr> + <tr> + <th>col_ds</th> + <td><p>Colors used for plotting the observed data and the +corresponding model prediction lines for the different datasets.</p></td> + </tr> + <tr> + <th>lty_ds</th> + <td><p>Line types to be used for the model predictions.</p></td> + </tr> + <tr> + <th>frame</th> + <td><p>Should a frame be drawn around the plots?</p></td> + </tr> + <tr> + <th>...</th> + <td><p>Further arguments passed to <code><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></code>.</p></td> + </tr> + </table> + + <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> + + <p>The function is called for its side effect.</p> + <h2 class="hasAnchor" id="author"><a class="anchor" href="#author"></a>Author</h2> + + <p>Johannes Ranke</p> + + <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> + <pre class="examples"><div class='input'><span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/lapply.html'>lapply</a></span><span class='op'>(</span><span class='va'>experimental_data_for_UBA_2019</span><span class='op'>[</span><span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>]</span>, + <span class='kw'>function</span><span class='op'>(</span><span class='va'>x</span><span class='op'>)</span> <span class='va'>x</span><span class='op'>$</span><span class='va'>data</span><span class='op'>[</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"name"</span>, <span class='st'>"time"</span>, <span class='st'>"value"</span><span class='op'>)</span><span class='op'>]</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/names.html'>names</a></span><span class='op'>(</span><span class='va'>ds</span><span class='op'>)</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/paste.html'>paste0</a></span><span class='op'>(</span><span class='st'>"ds "</span>, <span class='fl'>6</span><span class='op'>:</span><span class='fl'>10</span><span class='op'>)</span> +<span class='va'>dfop_sfo</span> <span class='op'><-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"DFOP"</span>, <span class='st'>"A1"</span><span class='op'>)</span>, + A1 <span class='op'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span><span class='op'>(</span><span class='st'>"SFO"</span><span class='op'>)</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='co'># \dontrun{</span> +<span class='va'>f</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='st'>"DFOP-SFO"</span> <span class='op'>=</span> <span class='va'>dfop_sfo</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>[</span>, <span class='fl'>3</span><span class='op'>:</span><span class='fl'>4</span><span class='op'>]</span>, standardized <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mixed.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='co'># For this fit we need to increase pnlsMaxiter, and we increase the</span> +<span class='co'># tolerance in order to speed up the fit for this example evaluation</span> +<span class='va'>f_nlme</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/nlme.html'>nlme</a></span><span class='op'>(</span><span class='va'>f</span>, control <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span>pnlsMaxIter <span class='op'>=</span> <span class='fl'>120</span>, tolerance <span class='op'>=</span> <span class='fl'>1e-3</span><span class='op'>)</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_nlme</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mixed.mmkin-2.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='va'>f_saem</span> <span class='op'><-</span> <span class='fu'><a href='saem.html'>saem</a></span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> +</div><div class='output co'>#> Running main SAEM algorithm +#> [1] "Mon Nov 9 17:18:17 2020" +#> .... +#> Minimisation finished +#> [1] "Mon Nov 9 17:18:26 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span><span class='va'>f_saem</span><span class='op'>)</span> +</div><div class='img'><img src='plot.mixed.mmkin-3.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># }</span> +</div></pre> + </div> + <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> + <nav id="toc" data-toggle="toc" class="sticky-top"> + <h2 data-toc-skip>Contents</h2> + </nav> + </div> +</div> + + + <footer> + <div class="copyright"> + <p>Developed by Johannes Ranke.</p> +</div> + +<div class="pkgdown"> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> +</div> + + </footer> + </div> + + + + + </body> +</html> + + diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index 26f4c3e3..f1b4c421 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -206,7 +206,8 @@ by the saemix function?</p></td> <h2 class="hasAnchor" id="value"><a class="anchor" href="#value"></a>Value</h2> <p>An S3 object of class 'saem.mmkin', containing the fitted -<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'.</p> +<a href='https://rdrr.io/pkg/saemix/man/SaemixObject-class.html'>saemix::SaemixObject</a> as a list component named 'so'. The +object also inherits from 'mixed.mmkin'.</p> <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixModel-class.html'>saemix::SaemixModel</a> object.</p> <p>An <a href='https://rdrr.io/pkg/saemix/man/SaemixData-class.html'>saemix::SaemixData</a> object.</p> <h2 class="hasAnchor" id="details"><a class="anchor" href="#details"></a>Details</h2> @@ -218,7 +219,7 @@ psi0 of <code><a href='https://rdrr.io/pkg/saemix/man/saemixModel.html'>saemix:: using <a href='mmkin.html'>mmkin</a>.</p> <h2 class="hasAnchor" id="see-also"><a class="anchor" href="#see-also"></a>See also</h2> - <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a></p></div> + <div class='dont-index'><p><a href='summary.saem.mmkin.html'>summary.saem.mmkin</a> <a href='plot.mixed.mmkin.html'>plot.mixed.mmkin</a></p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> <pre class="examples"><div class='input'><span class='co'># \dontrun{</span> @@ -229,27 +230,27 @@ using <a href='mmkin.html'>mmkin</a>.</p> state.ini <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>parent <span class='op'>=</span> <span class='fl'>100</span><span class='op'>)</span>, fixed_initials <span class='op'>=</span> <span class='st'>"parent"</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_p0_fixed</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_p0_fixed</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:11 2020" +#> [1] "Mon Nov 9 17:18:28 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:13 2020"</div><div class='input'> +#> [1] "Mon Nov 9 17:18:30 2020"</div><div class='input'> <span class='va'>f_mmkin_parent</span> <span class='op'><-</span> <span class='fu'><a href='mmkin.html'>mmkin</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span><span class='st'>"SFO"</span>, <span class='st'>"FOMC"</span>, <span class='st'>"DFOP"</span><span class='op'>)</span>, <span class='va'>ds</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> <span class='va'>f_saem_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:14 2020" +#> [1] "Mon Nov 9 17:18:31 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:16 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:18:33 2020"</div><div class='input'><span class='va'>f_saem_fomc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:16 2020" +#> [1] "Mon Nov 9 17:18:33 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:18 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:18:35 2020"</div><div class='input'><span class='va'>f_saem_dfop</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent</span><span class='op'>[</span><span class='st'>"DFOP"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:19 2020" +#> [1] "Mon Nov 9 17:18:36 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:22 2020"</div><div class='input'> +#> [1] "Mon Nov 9 17:18:39 2020"</div><div class='input'> <span class='co'># The returned saem.mmkin object contains an SaemixObject, therefore we can use</span> <span class='co'># functions from saemix</span> <span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'>saemix</span><span class='op'>)</span> @@ -295,10 +296,10 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='va'>f_mmkin_parent_tc</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_mmkin_parent</span>, error_model <span class='op'>=</span> <span class='st'>"tc"</span><span class='op'>)</span> <span class='va'>f_saem_fomc_tc</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin_parent_tc</span><span class='op'>[</span><span class='st'>"FOMC"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:24 2020" +#> [1] "Mon Nov 9 17:18:41 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:29 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:18:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/compare.saemix.html'>compare.saemix</a></span><span class='op'>(</span><span class='fu'><a href='https://rdrr.io/r/base/list.html'>list</a></span><span class='op'>(</span><span class='va'>f_saem_fomc</span><span class='op'>$</span><span class='va'>so</span>, <span class='va'>f_saem_fomc_tc</span><span class='op'>$</span><span class='va'>so</span><span class='op'>)</span><span class='op'>)</span> </div><div class='output co'>#> Likelihoods computed by importance sampling </div><div class='output co'>#> AIC BIC #> 1 467.7644 465.0305 #> 2 469.4862 466.3617</div><div class='input'> @@ -318,20 +319,20 @@ using <a href='mmkin.html'>mmkin</a>.</p> <span class='co'># solutions written for mkin this took around four minutes</span> <span class='va'>f_saem_sfo_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:31 2020" +#> [1] "Mon Nov 9 17:18:48 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:36 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:18:53 2020"</div><div class='input'><span class='va'>f_saem_dfop_sfo</span> <span class='op'><-</span> <span class='fu'>saem</span><span class='op'>(</span><span class='va'>f_mmkin</span><span class='op'>[</span><span class='st'>"DFOP-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> </div><div class='output co'>#> Running main SAEM algorithm -#> [1] "Mon Nov 9 09:03:37 2020" +#> [1] "Mon Nov 9 17:18:54 2020" #> .... #> Minimisation finished -#> [1] "Mon Nov 9 09:03:46 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> +#> [1] "Mon Nov 9 17:19:03 2020"</div><div class='input'><span class='fu'><a href='https://rdrr.io/pkg/saemix/man/summary-methods.html'>summary</a></span><span class='op'>(</span><span class='va'>f_saem_dfop_sfo</span>, data <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> </div><div class='output co'>#> saemix version used for fitting: 3.1.9000 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Mon Nov 9 09:03:47 2020 -#> Date of summary: Mon Nov 9 09:03:47 2020 +#> Date of fit: Mon Nov 9 17:19:04 2020 +#> Date of summary: Mon Nov 9 17:19:04 2020 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -346,7 +347,7 @@ using <a href='mmkin.html'>mmkin</a>.</p> #> #> Model predictions using solution type analytical #> -#> Fitted in 9.758 s using 300, 100 iterations +#> Fitted in 9.941 s using 300, 100 iterations #> #> Variance model: Constant variance #> diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index 5cfca07a..02fca7f9 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -148,6 +148,9 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/parms.html</loc> </url> <url> + <loc>https://pkgdown.jrwb.de/mkin/reference/plot.mixed.mmkin.html</loc> + </url> + <url> <loc>https://pkgdown.jrwb.de/mkin/reference/plot.mkinfit.html</loc> </url> <url> @@ -157,9 +160,6 @@ <loc>https://pkgdown.jrwb.de/mkin/reference/plot.nafta.html</loc> </url> <url> - <loc>https://pkgdown.jrwb.de/mkin/reference/plot_mixed.html</loc> - </url> - <url> <loc>https://pkgdown.jrwb.de/mkin/reference/print.mkinds.html</loc> </url> <url> diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 85bd74f6..9526a427 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -66,8 +66,8 @@ parameters taken from the mmkin object are used} \item{object}{An nlme.mmkin object to update} } \value{ -Upon success, a fitted nlme.mmkin object, which is an nlme object -with additional elements +Upon success, a fitted 'nlme.mmkin' object, which is an nlme object +with additional elements. It also inherits from 'mixed.mmkin'. } \description{ This functions sets up a nonlinear mixed effects model for an mmkin row @@ -150,5 +150,6 @@ endpoints(f_nlme_dfop) } } \seealso{ -\code{\link[=nlme_function]{nlme_function()}} +\code{\link[=nlme_function]{nlme_function()}}, \link{plot.mixed.mmkin}, \link{summary.nlme.mmkin}, +\link{parms.nlme.mmkin} } diff --git a/man/plot_mixed.Rd b/man/plot.mixed.mmkin.Rd index d3cee7c9..66e79f09 100644 --- a/man/plot_mixed.Rd +++ b/man/plot.mixed.mmkin.Rd @@ -1,33 +1,10 @@ % Generated by roxygen2: do not edit by hand -% Please edit documentation in R/plot_mixed.R -\name{plot_mixed} -\alias{plot_mixed} -\alias{plot.saem.mmkin} -\alias{plot.nlme.mmkin} +% Please edit documentation in R/plot.mixed.mmkin.R +\name{plot.mixed.mmkin} +\alias{plot.mixed.mmkin} \title{Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object} \usage{ -\method{plot}{saem.mmkin}( - x, - i = 1:ncol(x$mmkin), - obs_vars = names(x$mkinmod$map), - standardized = TRUE, - xlab = "Time", - xlim = range(x$data$time), - resplot = c("predicted", "time"), - ymax = "auto", - maxabs = "auto", - ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), - nrow.legend = ceiling((length(i) + 1)/ncol.legend), - rel.height.legend = 0.03 + 0.08 * nrow.legend, - rel.height.bottom = 1.1, - pch_ds = 1:length(i), - col_ds = pch_ds + 1, - lty_ds = col_ds, - frame = TRUE, - ... -) - -\method{plot}{nlme.mmkin}( +\method{plot}{mixed.mmkin}( x, i = 1:ncol(x$mmkin), obs_vars = names(x$mkinmod$map), @@ -93,7 +70,7 @@ corresponding model prediction lines for the different datasets.} \item{...}{Further arguments passed to \code{\link{plot}}.} } \value{ -The functions are called for their side effect. +The function is called for its side effect. } \description{ Plot predictions from a fitted nonlinear mixed model obtained via an mmkin row object @@ -108,7 +85,6 @@ dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE) plot(f[, 3:4], standardized = TRUE) -library(nlme) # For this fit we need to increase pnlsMaxiter, and we increase the # tolerance in order to speed up the fit for this example evaluation f_nlme <- nlme(f, control = list(pnlsMaxIter = 120, tolerance = 1e-3)) diff --git a/man/saem.Rd b/man/saem.Rd index 56b54fbf..17f777c4 100644 --- a/man/saem.Rd +++ b/man/saem.Rd @@ -44,7 +44,8 @@ by the saemix function?} } \value{ An S3 object of class 'saem.mmkin', containing the fitted -\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. +\link[saemix:SaemixObject-class]{saemix::SaemixObject} as a list component named 'so'. The +object also inherits from 'mixed.mmkin'. An \link[saemix:SaemixModel-class]{saemix::SaemixModel} object. @@ -114,5 +115,5 @@ summary(f_saem_dfop_sfo, data = FALSE) } } \seealso{ -\link{summary.saem.mmkin} +\link{summary.saem.mmkin} \link{plot.mixed.mmkin} } |
