diff options
21 files changed, 121 insertions, 115 deletions
@@ -48,8 +48,12 @@ #' start = mean_dp) #' summary(m_nlme) #' plot(augPred(m_nlme, level = 0:1), layout = c(3, 1)) -#' # augPred does not seem to work on fits with more than one state +#' # augPred does not work on fits with more than one state #' # variable +#' # +#' # The procedure is greatly simplified by the nlme.mmkin function +#' f_nlme <- nlme(f) +#' plot(f_nlme) #' #' @return A function that can be used with nlme #' @export diff --git a/R/nlme.mmkin.R b/R/nlme.mmkin.R index 22a70f18..d3369cf5 100644 --- a/R/nlme.mmkin.R +++ b/R/nlme.mmkin.R @@ -55,6 +55,7 @@ get_deg_func <- function() { #' print(f_nlme_dfop) #' plot(f_nlme_dfop) #' endpoints(f_nlme_dfop) +#' #' \dontrun{ #' f_nlme_2 <- nlme(f["SFO", ], start = c(parent_0 = 100, log_k_parent = 0.1)) #' update(f_nlme_2, random = parent_0 ~ 1) @@ -101,6 +102,7 @@ get_deg_func <- function() { #' AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc) #' print(f_nlme_dfop_tc) #' } +#' #' f_2_obs <- mmkin(list("SFO-SFO" = m_sfo_sfo, #' "DFOP-SFO" = m_dfop_sfo), #' ds_2, quiet = TRUE, error_model = "obs") diff --git a/R/plot.nlme.mmkin.R b/R/plot.nlme.mmkin.R index a27f0caa..afb682a7 100644 --- a/R/plot.nlme.mmkin.R +++ b/R/plot.nlme.mmkin.R @@ -5,11 +5,10 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' @param x An object of class \code{\link{nlme.mmkin}} #' @param i A numeric index to select datasets for which to plot the nlme fit, #' in case plots get too large -#' @param main The main title placed on the outer margin of the plot. #' @inheritParams plot.mkinfit -#' @param legends An index for the fits for which legends should be shown. #' @param standardized Should the residuals be standardized? Only takes effect if #' `resplot = "time"`. +#' @param rel.height.legend The relative height of the legend shown on top #' @param rel.height.bottom The relative height of the bottom plot row #' @param ymax Vector of maximum y axis values #' @param \dots Further arguments passed to \code{\link{plot.mkinfit}} and @@ -31,6 +30,7 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' A1 = mkinsub("SFO"), quiet = TRUE) #' f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1) #' 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 @@ -38,15 +38,15 @@ if(getRversion() >= '2.15.1') utils::globalVariables("ds") #' plot(f_nlme) #' @export plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), - main = NULL, obs_vars = names(x$mkinmod$map), standardized = TRUE, xlab = "Time", xlim = range(x$data$time), - legends = 1, - lpos = "topright", inset = c(0.05, 0.05), resplot = c("predicted", "time"), ymax = "auto", maxabs = "auto", + ncol.legend = ifelse(length(i) <= 3, length(i) + 1, ifelse(length(i) <= 8, 3, 4)), + nrow.legend = ceiling((length(i) + 1) / ncol.legend), + rel.height.legend = 0.03 + 0.08 * nrow.legend, rel.height.bottom = 1.1, pch_ds = 1:length(i), col_ds = pch_ds + 1, @@ -65,7 +65,7 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), names(degparms_fixed) <- rownames(fit_1$fixed) degparms_all <- cbind(as.matrix(degparms_optim), matrix(rep(degparms_fixed, nrow(degparms_optim)), - ncol = length(degparms_fixed), + ncol = length(degparms_fixed), nrow = nrow(degparms_optim), byrow = TRUE)) degparms_all_names <- c(degparms_optim_names, names(degparms_fixed)) colnames(degparms_all) <- degparms_all_names @@ -81,14 +81,27 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), n_plot_rows = length(obs_vars) n_plots = n_plot_rows * 2 - # Set relative plot heights, so the first and the last plot are the norm - # and the middle plots (if n_plot_rows >2) are smaller by rel.height.middle - rel.heights <- if (n_plot_rows > 1) c(rep(1, n_plot_rows - 1), rel.height.bottom) else 1 + # 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(1:n_plots, - n_plot_rows, 2, byrow = TRUE) + 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$time, @@ -96,6 +109,7 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), pred_ds <- purrr::map_dfr(i, function(ds_i) { odeparms_trans <- degparms_all[ds_i, odeparms_names] + names(odeparms_trans) <- odeparms_names # needed if only one odeparm odeparms <- backtransform_odeparms(odeparms_trans, x$mkinmod, transform_rates = fit_1$transform_rates, @@ -162,14 +176,6 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), col = col_ds[ds_i], lty = lty_ds[ds_i]) } - if (plot_row %in% legends) { - legend(lpos, inset = inset, - legend = c("Population", ds_names[i]), - lty = c(1, lty_ds), lwd = c(2, rep(1, length(i))), - col = c(1, col_ds), - pch = c(NA, pch_ds)) - } - if (identical(maxabs, "auto")) { maxabs = max(abs(observed_row$residual), na.rm = TRUE) } @@ -194,6 +200,8 @@ plot.nlme.mmkin <- function(x, i = 1:ncol(x$mmkin_orig), ylim = c(-1.2 * maxabs, 1.2 * maxabs), ylab = if (standardized) "Standardized residual" else "Residual") + abline(h = 0, lty = 2) + for (ds_i in seq_along(i)) { observed_row_ds <- merge( subset(observed_row, ds == ds_names[ds_i], c("time", "residual")), diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index d6c3d6c9..8f493a24 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: 2020-10-24T00:14Z +last_built: 2020-10-26T13:18Z 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 bf7c274a..cfc5bc2b 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 965d4620..8e2eb70d 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 057b525f..0b173f9e 100644 --- a/docs/dev/reference/Rplot003.png +++ b/docs/dev/reference/Rplot003.png diff --git a/docs/dev/reference/Rplot004.png b/docs/dev/reference/Rplot004.png Binary files differindex 2b5ba960..4874cd19 100644 --- a/docs/dev/reference/Rplot004.png +++ b/docs/dev/reference/Rplot004.png diff --git a/docs/dev/reference/nlme-1.png b/docs/dev/reference/nlme-1.png Binary files differindex 8db1f999..0b34db8f 100644 --- a/docs/dev/reference/nlme-1.png +++ b/docs/dev/reference/nlme-1.png diff --git a/docs/dev/reference/nlme-2.png b/docs/dev/reference/nlme-2.png Binary files differnew file mode 100644 index 00000000..ce932c86 --- /dev/null +++ b/docs/dev/reference/nlme-2.png diff --git a/docs/dev/reference/nlme.html b/docs/dev/reference/nlme.html index af5a151a..e21074e7 100644 --- a/docs/dev/reference/nlme.html +++ b/docs/dev/reference/nlme.html @@ -75,7 +75,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> </button> <span class="navbar-brand"> <a class="navbar-link" href="../index.html">mkin</a> - <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.3</span> + <span class="version label label-info" data-toggle="tooltip" data-placement="bottom" title="In-development version">0.9.50.4</span> </span> </div> @@ -123,7 +123,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> </ul> <ul class="nav navbar-nav navbar-right"> <li> - <a href="http://github.com/jranke/mkin/"> + <a href="https://github.com/jranke/mkin/"> <span class="fab fa fab fa-github fa-lg"></span> </a> @@ -142,7 +142,7 @@ datasets. They are used internally by the nlme.mmkin() method." /> <div class="col-md-9 contents"> <div class="page-header"> <h1>Helper functions to create nlme models from mmkin row objects</h1> - <small class="dont-index">Source: <a href='http://github.com/jranke/mkin/blob/master/R/nlme.R'><code>R/nlme.R</code></a></small> + <small class="dont-index">Source: <a href='https://github.com/jranke/mkin/blob/master/R/nlme.R'><code>R/nlme.R</code></a></small> <div class="hidden name"><code>nlme.Rd</code></div> </div> @@ -153,11 +153,11 @@ objects that have been obtained by fitting the same model to a list of datasets. They are used internally by the <code><a href='nlme.mmkin.html'>nlme.mmkin()</a></code> method.</p> </div> - <pre class="usage"><span class='fu'>nlme_function</span>(<span class='no'>object</span>) + <pre class="usage"><span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span> -<span class='fu'>mean_degparms</span>(<span class='no'>object</span>, <span class='kw'>random</span> <span class='kw'>=</span> <span class='fl'>FALSE</span>) +<span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>object</span>, random <span class='op'>=</span> <span class='cn'>FALSE</span><span class='op'>)</span> -<span class='fu'>nlme_data</span>(<span class='no'>object</span>)</pre> +<span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>object</span><span class='op'>)</span></pre> <h2 class="hasAnchor" id="arguments"><a class="anchor" href="#arguments"></a>Arguments</h2> <table class="ref-arguments"> @@ -185,71 +185,77 @@ nlme for the case of a single grouping variable ds.</p> <div class='dont-index'><p><code><a href='nlme.mmkin.html'>nlme.mmkin</a></code></p></div> <h2 class="hasAnchor" id="examples"><a class="anchor" href="#examples"></a>Examples</h2> - <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</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</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</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>) + <pre class="examples"><div class='input'><span class='va'>sampling_times</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='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='op'>)</span> +<span class='va'>m_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'>"SFO"</span><span class='op'>)</span><span class='op'>)</span> +<span class='va'>d_SFO_1</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.1</span><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'>98</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> +<span class='va'>d_SFO_1_long</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>d_SFO_1</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> +<span class='va'>d_SFO_2</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.05</span><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'>102</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> +<span class='va'>d_SFO_2_long</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>d_SFO_2</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> +<span class='va'>d_SFO_3</span> <span class='op'><-</span> <span class='fu'><a href='mkinpredict.html'>mkinpredict</a></span><span class='op'>(</span><span class='va'>m_SFO</span>, + <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>k_parent <span class='op'>=</span> <span class='fl'>0.02</span><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'>103</span><span class='op'>)</span>, <span class='va'>sampling_times</span><span class='op'>)</span> +<span class='va'>d_SFO_3_long</span> <span class='op'><-</span> <span class='fu'><a href='mkin_wide_to_long.html'>mkin_wide_to_long</a></span><span class='op'>(</span><span class='va'>d_SFO_3</span>, time <span class='op'>=</span> <span class='st'>"time"</span><span class='op'>)</span> + +<span class='va'>d1</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_SFO_1</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>3</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +<span class='va'>d2</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_SFO_2</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>2</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +<span class='va'>d3</span> <span class='op'><-</span> <span class='fu'><a href='add_err.html'>add_err</a></span><span class='op'>(</span><span class='va'>d_SFO_3</span>, <span class='kw'>function</span><span class='op'>(</span><span class='va'>value</span><span class='op'>)</span> <span class='fl'>4</span>, n <span class='op'>=</span> <span class='fl'>1</span><span class='op'>)</span> +<span class='va'>ds</span> <span class='op'><-</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span><span class='op'>(</span>d1 <span class='op'>=</span> <span class='va'>d1</span>, d2 <span class='op'>=</span> <span class='va'>d2</span>, d3 <span class='op'>=</span> <span class='va'>d3</span><span class='op'>)</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='st'>"SFO"</span>, <span class='va'>ds</span>, cores <span class='op'>=</span> <span class='fl'>1</span>, quiet <span class='op'>=</span> <span class='cn'>TRUE</span><span class='op'>)</span> +<span class='va'>mean_dp</span> <span class='op'><-</span> <span class='fu'>mean_degparms</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> +<span class='va'>grouped_data</span> <span class='op'><-</span> <span class='fu'>nlme_data</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> +<span class='va'>nlme_f</span> <span class='op'><-</span> <span class='fu'>nlme_function</span><span class='op'>(</span><span class='va'>f</span><span class='op'>)</span> <span class='co'># These assignments are necessary for these objects to be</span> <span class='co'># visible to nlme and augPred when evaluation is done by</span> <span class='co'># pkgdown to generated the html docs.</span> -<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"nlme_f"</span>, <span class='no'>nlme_f</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span>()) -<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span>(<span class='st'>"grouped_data"</span>, <span class='no'>grouped_data</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></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>) -<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'>#> Nonlinear mixed-effects model fit by maximum likelihood +<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"nlme_f"</span>, <span class='va'>nlme_f</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/assign.html'>assign</a></span><span class='op'>(</span><span class='st'>"grouped_data"</span>, <span class='va'>grouped_data</span>, <span class='fu'><a href='https://rdrr.io/r/base/environment.html'>globalenv</a></span><span class='op'>(</span><span class='op'>)</span><span class='op'>)</span> + +<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> +<span class='va'>m_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'>value</span> <span class='op'>~</span> <span class='fu'>nlme_f</span><span class='op'>(</span><span class='va'>name</span>, <span class='va'>time</span>, <span class='va'>parent_0</span>, <span class='va'>log_k_parent_sink</span><span class='op'>)</span>, + data <span class='op'>=</span> <span class='va'>grouped_data</span>, + fixed <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>+</span> <span class='va'>log_k_parent_sink</span> <span class='op'>~</span> <span class='fl'>1</span>, + random <span class='op'>=</span> <span class='fu'><a href='https://rdrr.io/pkg/nlme/man/pdDiag.html'>pdDiag</a></span><span class='op'>(</span><span class='va'>parent_0</span> <span class='op'>+</span> <span class='va'>log_k_parent_sink</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span>, + start <span class='op'>=</span> <span class='va'>mean_dp</span><span class='op'>)</span> +<span class='fu'><a href='https://rdrr.io/r/base/summary.html'>summary</a></span><span class='op'>(</span><span class='va'>m_nlme</span><span class='op'>)</span> +</div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood #> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) #> Data: grouped_data #> AIC BIC logLik -#> 252.7798 262.1358 -121.3899 +#> 298.2781 307.7372 -144.1391 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent_sink Residual -#> StdDev: 0.0006768135 0.6800777 2.489397 +#> parent_0 log_k_parent_sink Residual +#> StdDev: 0.9374733 0.7098105 3.83543 #> #> Fixed effects: parent_0 + log_k_parent_sink ~ 1 -#> Value Std.Error DF t-value p-value -#> parent_0 101.74884 0.6456014 44 157.60321 0 -#> log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0 +#> Value Std.Error DF t-value p-value +#> parent_0 101.76838 1.1445444 45 88.91606 0 +#> log_k_parent_sink -3.05444 0.4195622 45 -7.28008 0 #> Correlation: #> prnt_0 -#> log_k_parent_sink 0.026 +#> log_k_parent_sink 0.034 #> #> Standardized Within-Group Residuals: #> Min Q1 Med Q3 Max -#> -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864 +#> -2.6169360 -0.2185329 0.0574070 0.5720937 3.0459868 #> -#> Number of Observations: 48 -#> Number of Groups: 3 </div><div class='input'><span class='fu'><a href='https://rdrr.io/r/base/plot.html'>plot</a></span>(<span class='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span>(<span class='no'>m_nlme</span>, <span class='kw'>level</span> <span class='kw'>=</span> <span class='fl'>0</span>:<span class='fl'>1</span>), <span class='kw'>layout</span> <span class='kw'>=</span> <span class='fu'><a href='https://rdrr.io/r/base/c.html'>c</a></span>(<span class='fl'>3</span>, <span class='fl'>1</span>))</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'># augPred does not seem to work on fits with more than one state -# variable - +#> Number of Observations: 49 +#> Number of Groups: 3 </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='fu'><a href='https://rdrr.io/pkg/nlme/man/augPred.html'>augPred</a></span><span class='op'>(</span><span class='va'>m_nlme</span>, level <span class='op'>=</span> <span class='fl'>0</span><span class='op'>:</span><span class='fl'>1</span><span class='op'>)</span>, layout <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='fl'>3</span>, <span class='fl'>1</span><span class='op'>)</span><span class='op'>)</span> +</div><div class='img'><img src='nlme-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='co'># augPred does not work on fits with more than one state</span> +<span class='co'># variable</span> +<span class='co'>#</span> +<span class='co'># The procedure is greatly simplified by the nlme.mmkin function</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><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='nlme-2.png' alt='' width='700' height='433' /></div><div class='input'> </div></pre> </div> <div class="col-md-3 hidden-xs hidden-sm" id="pkgdown-sidebar"> @@ -266,7 +272,7 @@ nlme for the case of a single grouping variable ds.</p> </div> <div class="pkgdown"> - <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.5.1.</p> + <p>Site built with <a href="https://pkgdown.r-lib.org/">pkgdown</a> 1.6.1.</p> </div> </footer> diff --git a/docs/dev/reference/nlme.mmkin-1.png b/docs/dev/reference/nlme.mmkin-1.png Binary files differindex d0a1d7d4..04d8b234 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-2.png b/docs/dev/reference/nlme.mmkin-2.png Binary files differindex b68dc3e0..c314c149 100644 --- a/docs/dev/reference/nlme.mmkin-2.png +++ b/docs/dev/reference/nlme.mmkin-2.png diff --git a/docs/dev/reference/nlme.mmkin-3.png b/docs/dev/reference/nlme.mmkin-3.png Binary files differindex 77804b2c..281d6024 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 96717087..d504e8f0 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 3c84abe2..90aec9be 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>, @@ -291,7 +291,8 @@ with additional elements</p> </div><div class='output co'>#> $distimes #> DT50 DT90 DT50back DT50_k1 DT50_k2 #> parent 10.79857 100.7937 30.34193 4.193938 43.85443 -#> </div><div class='input'><span class='co'># \dontrun{</span> +#> </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> <span class='fu'><a href='https://rdrr.io/r/stats/update.html'>update</a></span><span class='op'>(</span><span class='va'>f_nlme_2</span>, random <span class='op'>=</span> <span class='va'>parent_0</span> <span class='op'>~</span> <span class='fl'>1</span><span class='op'>)</span> </div><div class='output co'>#> Nonlinear mixed-effects model fit by maximum likelihood @@ -416,7 +417,8 @@ with additional elements</p> #> const prop #> 2.23222625 0.01262414 #> Number of Observations: 90 -#> Number of Groups: 5 </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>, +#> Number of Groups: 5 </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> <span class='va'>f_nlme_sfo_sfo_obs</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_2_obs</span><span class='op'>[</span><span class='st'>"SFO-SFO"</span>, <span class='op'>]</span><span class='op'>)</span> diff --git a/docs/dev/reference/plot.nlme.mmkin-2.png b/docs/dev/reference/plot.nlme.mmkin-2.png Binary files differindex 4ec26146..7b59b947 100644 --- a/docs/dev/reference/plot.nlme.mmkin-2.png +++ b/docs/dev/reference/plot.nlme.mmkin-2.png diff --git a/docs/dev/reference/plot.nlme.mmkin.html b/docs/dev/reference/plot.nlme.mmkin.html index c633e15a..afd9d8d0 100644 --- a/docs/dev/reference/plot.nlme.mmkin.html +++ b/docs/dev/reference/plot.nlme.mmkin.html @@ -151,17 +151,16 @@ <span class='fu'><a href='https://rdrr.io/r/graphics/plot.default.html'>plot</a></span><span class='op'>(</span> <span class='va'>x</span>, i <span 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_orig</span><span class='op'>)</span>, - main <span class='op'>=</span> <span class='cn'>NULL</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>, - legends <span class='op'>=</span> <span class='fl'>1</span>, - lpos <span class='op'>=</span> <span class='st'>"topright"</span>, - inset <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='fl'>0.05</span>, <span class='fl'>0.05</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>, @@ -183,10 +182,6 @@ in case plots get too large</p></td> </tr> <tr> - <th>main</th> - <td><p>The main title placed on the outer margin of the plot.</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 @@ -206,20 +201,6 @@ variables in the model.</p></td> <td><p>Plot range in x direction.</p></td> </tr> <tr> - <th>legends</th> - <td><p>An index for the fits for which legends should be shown.</p></td> - </tr> - <tr> - <th>lpos</th> - <td><p>Position(s) of the legend(s). Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> as -the first argument. If not length one, this should be of the same length -as the obs_var argument.</p></td> - </tr> - <tr> - <th>inset</th> - <td><p>Passed to <code><a href='https://rdrr.io/r/graphics/legend.html'>legend</a></code> if applicable.</p></td> - </tr> - <tr> <th>resplot</th> <td><p>Should the residuals plotted against time or against predicted values?</p></td> @@ -234,6 +215,10 @@ predicted values?</p></td> scaling of the y axis and defaults to "auto".</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> @@ -276,7 +261,8 @@ corresponding model prediction lines for the different datasets.</p></td> 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='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>, cores <span class='op'>=</span> <span class='fl'>1</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.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'><span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> +</div><div class='img'><img src='plot.nlme.mmkin-1.png' alt='' width='700' height='433' /></div><div class='input'> +<span class='kw'><a href='https://rdrr.io/r/base/library.html'>library</a></span><span class='op'>(</span><span class='va'><a href='https://svn.r-project.org/R-packages/trunk/nlme/'>nlme</a></span><span class='op'>)</span> <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> diff --git a/man/nlme.Rd b/man/nlme.Rd index 2ee2a20c..df721a0f 100644 --- a/man/nlme.Rd +++ b/man/nlme.Rd @@ -72,8 +72,12 @@ m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), start = mean_dp) summary(m_nlme) plot(augPred(m_nlme, level = 0:1), layout = c(3, 1)) -# augPred does not seem to work on fits with more than one state +# augPred does not work on fits with more than one state # variable +# +# The procedure is greatly simplified by the nlme.mmkin function +f_nlme <- nlme(f) +plot(f_nlme) } \seealso{ diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd index 87d84c74..041b939a 100644 --- a/man/nlme.mmkin.Rd +++ b/man/nlme.mmkin.Rd @@ -85,6 +85,7 @@ AIC(f_nlme_sfo, f_nlme_dfop) print(f_nlme_dfop) plot(f_nlme_dfop) endpoints(f_nlme_dfop) + \dontrun{ f_nlme_2 <- nlme(f["SFO", ], start = c(parent_0 = 100, log_k_parent = 0.1)) update(f_nlme_2, random = parent_0 ~ 1) @@ -131,6 +132,7 @@ endpoints(f_nlme_dfop) AIC(f_nlme_sfo, f_nlme_sfo_tc, f_nlme_dfop, f_nlme_dfop_tc) print(f_nlme_dfop_tc) } + f_2_obs <- mmkin(list("SFO-SFO" = m_sfo_sfo, "DFOP-SFO" = m_dfop_sfo), ds_2, quiet = TRUE, error_model = "obs") diff --git a/man/plot.nlme.mmkin.Rd b/man/plot.nlme.mmkin.Rd index 5f6e4ed3..6944d4b1 100644 --- a/man/plot.nlme.mmkin.Rd +++ b/man/plot.nlme.mmkin.Rd @@ -7,17 +7,16 @@ \method{plot}{nlme.mmkin}( x, i = 1:ncol(x$mmkin_orig), - main = NULL, obs_vars = names(x$mkinmod$map), standardized = TRUE, xlab = "Time", xlim = range(x$data$time), - legends = 1, - lpos = "topright", - inset = c(0.05, 0.05), 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, @@ -32,8 +31,6 @@ \item{i}{A numeric index to select datasets for which to plot the nlme fit, in case plots get too large} -\item{main}{The main title placed on the outer margin of the plot.} - \item{obs_vars}{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.} @@ -45,14 +42,6 @@ variables in the model.} \item{xlim}{Plot range in x direction.} -\item{legends}{An index for the fits for which legends should be shown.} - -\item{lpos}{Position(s) of the legend(s). Passed to \code{\link{legend}} as -the first argument. If not length one, this should be of the same length -as the obs_var argument.} - -\item{inset}{Passed to \code{\link{legend}} if applicable.} - \item{resplot}{Should the residuals plotted against time or against predicted values?} @@ -61,6 +50,8 @@ predicted values?} \item{maxabs}{Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto".} +\item{rel.height.legend}{The relative height of the legend shown on top} + \item{rel.height.bottom}{The relative height of the bottom plot row} \item{pch_ds}{Symbols to be used for plotting the data.} @@ -89,6 +80,7 @@ dfop_sfo <- mkinmod(parent = mkinsub("DFOP", "A1"), A1 = mkinsub("SFO"), quiet = TRUE) f <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, cores = 1) 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 |
