Subsetting and plotting for mmkin objects

Including documentation and documentation improvements for mmkin().

2 files changed, 107 insertions, 0 deletions

diff --git a/R/mmkin.R b/R/mmkin.R
index 1e1c4a33..be4526af 100644
--- a/R/mmkin.R
+++ b/R/mmkin.R
@@ -1,3 +1,24 @@
+# Copyright (C) 2015 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+# The summary function is an adapted and extended version of summary.modFit
+# from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn
+# inspired by summary.nls.lm
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
 mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets, 
                   cores = round(detectCores()/2), cluster = NULL, ...) 
 {
@@ -44,3 +65,10 @@ mmkin <- function(models = c("SFO", "FOMC", "DFOP"), datasets,
   class(results) <- "mmkin"
   return(results)
 }
+
+"[.mmkin" <- function(x, i, j, ..., drop = FALSE) {
+  class(x) <- NULL
+  x_sub <- x[i, j, drop = drop]
+  if (!drop) class(x_sub) <- "mmkin"
+  return(x_sub)
+}
diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R
new file mode 100644
index 00000000..036ec59f
--- /dev/null
+++ b/R/plot.mmkin.R
@@ -0,0 +1,79 @@
+# Copyright (C) 2015 Johannes Ranke
+# Contact: jranke@uni-bremen.de
+# The summary function is an adapted and extended version of summary.modFit
+# from the FME package, v 1.1 by Soetart and Petzoldt, which was in turn
+# inspired by summary.nls.lm
+
+# This file is part of the R package mkin
+
+# mkin is free software: you can redistribute it and/or modify it under the
+# terms of the GNU General Public License as published by the Free Software
+# Foundation, either version 3 of the License, or (at your option) any later
+# version.
+
+# This program is distributed in the hope that it will be useful, but WITHOUT
+# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
+# FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+# details.
+
+# You should have received a copy of the GNU General Public License along with
+# this program. If not, see <http://www.gnu.org/licenses/>
+
+plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", errmin_digits = 2, 
+                       cex = 0.7, rel.height.middle = 0.9, ...) {
+  n.m <- nrow(x)
+  n.d <- ncol(x)
+  if (n.m > 1 & n.d > 1) stop("Please select fits either for one model or for one dataset")
+  if (n.m == 1 & n.d == 1) loop_over = "none"
+  if (n.m > 1) loop_over <- "models"
+  if (n.d > 1) loop_over <- "datasets"
+  n.fits <- length(x)
+
+  if (main == "auto") {
+    main = switch(loop_over,
+                  none = paste(rownames(x), colnames(x)),
+                  models = colnames(x),
+                  datasets = rownames(x))
+  }
+
+  oldpar <- par(no.readonly = TRUE)
+  rel.heights <- if (n.fits > 2) c(1, rep(rel.height.middle, n.fits - 2), 1)
+                 else rep(1, n.fits)
+  layout(matrix(1:(2 * n.fits), n.fits, 2, byrow = TRUE), heights = rel.heights)
+
+  #par(mfrow = c(n.fits, 2))
+  par(mar = c(3.0, 4.1, 4.1, 2.1)) # Reduce bottom margin by 2.1 - hides x axis legend
+  par(cex = cex)
+
+  for (i.fit in 1:n.fits) {
+    if (i.fit == 2) {
+      # Reduce top margin by 2 after the first plot as we have no main title, 
+      # reduced plot height, therefore we need rel.height.middle in the layout
+      par(mar = c(3.0, 4.1, 2.1, 2.1))
+    }
+    if (i.fit == n.fits) {
+      # Reduce top margin by 2 after the first plot as we have no main title, 
+      # plot height remains about constant
+      par(mar = c(5.1, 4.1, 2.1, 2.1))
+
+    }
+    fit <- x[[i.fit]]
+    plot(fit, legend = legends == i.fit, ...)
+
+    title(main, outer = TRUE, line = -2)
+
+    fit_name <- switch(loop_over,
+                       models = rownames(x)[i.fit],
+                       datasets = colnames(x)[i.fit],
+                       none = "") 
+
+    if (!is.null(errmin_var)) {
+      chi2 <- paste0(round(100 * mkinerrmin(fit)[errmin_var, "err.min"], errmin_digits), "%")
+      mtext(bquote(.(fit_name) ~ chi^2 ~ "error level" == .(chi2)), cex = cex, line = 0.4)
+    }
+    mkinresplot(fit, legend = FALSE, ...)
+    mtext(paste(fit_name, "residuals"), cex = cex, line = 0.4)
+  }
+
+  par(oldpar, no.readonly = TRUE)
+}