Fix the plot margins for combined plots

5 files changed, 49 insertions, 11 deletions

diff --git a/R/plot.mkinfit.R b/R/plot.mkinfit.R
index 317c74a3..58ff88bc 100644
--- a/R/plot.mkinfit.R
+++ b/R/plot.mkinfit.R
@@ -103,6 +103,27 @@ plot.mkinfit <- function(x, fit = x,
       ylim_row = ylim
     }
 
+    if (sep_obs) {
+      # Margins for top row of plots when we have more than one row
+      # Reduce bottom margin by 2.1 - hides x axis legend
+      if (plot_row == 1 & n_plot_rows > 1) {
+        par(mar = c(3.0, 4.1, 4.1, 2.1)) 
+      }
+
+      # Margins for middle rows of plots, if any
+      if (plot_row > 1 & plot_row < n_plot_rows) {
+        # 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))
+      }
+
+      # Margins for bottom row of plots when we have more than one row
+      if (plot_row == n_plot_rows & n_plot_rows > 1) {
+        # Restore bottom margin for last plot to show x axis legend
+        par(mar = c(5.1, 4.1, 2.1, 2.1))
+      }
+    }
+
     # Set up the main plot if not to be added to an existing plot
     if (add == FALSE) {
       plot(0, type="n", 
diff --git a/R/plot.mmkin.R b/R/plot.mmkin.R
index 7b54be4b..2cbb4a79 100644
--- a/R/plot.mmkin.R
+++ b/R/plot.mmkin.R
@@ -46,15 +46,29 @@ plot.mmkin <- function(x, main = "auto", legends = 1, errmin_var = "All data", e
                  else rep(1, n.fits)
   layout(matrix(1:(2 * n.fits), n.fits, 2, byrow = TRUE), heights = rel.heights)
 
-  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) {
+
+    # Margins for top row of plots when we have more than one row
+    # Reduce bottom margin by 2.1 - hides x axis legend
+    if (i.fit == 1 & n.fits > 1) {
+      par(mar = c(3.0, 4.1, 4.1, 2.1)) 
+    }
+
+    # Margins for middle rows of plots, if any
+    if (i.fit > 1 & i.fit < n.fits) {
       # 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))
     }
+
+    # Margins for bottom row of plots when we have more than one row
+    if (i.fit == n.fits & n.fits > 1) {
+      # Restore bottom margin for last plot to show x axis legend
+      par(mar = c(5.1, 4.1, 2.1, 2.1))
+    }
+
     fit <- x[[i.fit]]
     plot(fit, legend = legends == i.fit, ...)
 
diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index 44caf8d2..d088e804 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -45,16 +45,17 @@ mmkin(models, datasets,
 }
 \examples{
 \dontrun{
-m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
-                           M1 = list(type = "SFO", to = "M2"),
-                           M2 = list(type = "SFO"), use_of_ff = "max")
+m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+                           M1 = mkinsub("SFO", "M2"),
+                           M2 = mkinsub("SFO"), use_of_ff = "max")
 
-m_synth_FOMC_lin <- mkinmod(parent = list(type = "FOMC", to = "M1"),
-                           M1 = list(type = "SFO", to = "M2"),
-                           M2 = list(type = "SFO"), use_of_ff = "max")
+m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),
+                            M1 = mkinsub("SFO", "M2"),
+                            M2 = mkinsub("SFO"), use_of_ff = "max")
 
 models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
 datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
+names(datasets) <- paste("Dataset", 1:3)
 
 time_default <- system.time(fits.0 <- mmkin(models, datasets))
 time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))
@@ -66,9 +67,11 @@ endpoints(fits[["SFO_lin", 2]])
 
 # Plot.mkinfit handles rows or columns of mmkin result objects
 plot(fits.0[1, ])
+plot(fits.0[, 1])
 # Double brackets to select a single mkinfit object, which will be
 # plotted by plot.mkinfit
 plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE)
+plot(fits.0[1, 1])
 }
 }
 \keyword{ optimize }
diff --git a/man/plot.mkinfit.Rd b/man/plot.mkinfit.Rd
index 00b2eca5..bc0b85e8 100644
--- a/man/plot.mkinfit.Rd
+++ b/man/plot.mkinfit.Rd
@@ -18,7 +18,7 @@
   lty_obs = rep(1, length(obs_vars)),
   add = FALSE, legend = !add,
   show_residuals = FALSE, maxabs = "auto",
-  sep_vars = FALSE, rel.height.middle = 0.9,
+  sep_obs = FALSE, rel.height.middle = 0.9,
   lpos = "topright", inset = c(0.05, 0.05), \dots)
 }
 \arguments{
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index ffd83d2f..37d7a25a 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -45,9 +45,9 @@
   Johannes Ranke
 }
 \examples{
-  # Only use one core not to offend CRAN checks
+  # Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed
   fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), 
-                cores = 1, quiet = TRUE)
+                cores = 1, quiet = TRUE, method.modFit = "Marq")
   plot(fits[, "FOCUS C"])
   plot(fits["FOMC", ])