From 43c0ae8431440bab723b35909d43f51434288c33 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Sat, 25 Jun 2016 21:07:11 +0200
Subject: Fix the plot margins for combined plots

---
 man/mmkin.Rd        | 15 +++++++++------
 man/plot.mkinfit.Rd |  2 +-
 man/plot.mmkin.Rd   |  4 ++--
 3 files changed, 12 insertions(+), 9 deletions(-)

(limited to 'man')

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", ])
 
-- 
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