From 9d6a975a0e3850a36889a18b5d9929d27b901ab3 Mon Sep 17 00:00:00 2001
From: Johannes Ranke <jranke@uni-bremen.de>
Date: Mon, 4 Mar 2019 14:09:45 +0100
Subject: Make some example output more reproducible

In order to avoid some unnecessary documentation rebuilds
---
 man/Extract.mmkin.Rd      |  5 -----
 man/mccall81_245T.Rd      |  6 ++++--
 man/transform_odeparms.Rd | 18 ++++++++++++++----
 3 files changed, 18 insertions(+), 11 deletions(-)

(limited to 'man')

diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd
index e27e83a0..973dc28f 100644
--- a/man/Extract.mmkin.Rd
+++ b/man/Extract.mmkin.Rd
@@ -37,9 +37,4 @@
     # This extracts an mkinfit object with lots of components
     fits[["FOMC", "B"]] 
   )
-
-  head(
-  # The same can be achieved by
-    fits["SFO", "B", drop = TRUE]
-  )
 }
diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd
index 0ea8af63..22368d6d 100644
--- a/man/mccall81_245T.Rd
+++ b/man/mccall81_245T.Rd
@@ -33,13 +33,15 @@
                          anisole = list(type = "SFO"))
   \dontrun{
     fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-    summary(fit.1, data = FALSE)
+    summary(fit.1)$bpar
+    endpoints(fit.1)
     # No convergence, no covariance matrix ...
     # k_phenol_sink is really small, therefore fix it to zero
     fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                    parms.ini = c(k_phenol_sink = 0),
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
-    summary(fit.2, data = FALSE)
+    summary(fit.2)$bpar
+    endpoints(fit.1)
   }
 }
 \keyword{datasets}
diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index a1ccdf26..006897d6 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -66,11 +66,17 @@ SFO_SFO <- mkinmod(
   m1 = list(type = "SFO"))
 # Fit the model to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
+fit.s <- summary(fit)
+# Transformed and backtransformed parameters
+print(fit.s$par, 3)
+print(fit.s$bpar, 3)
 
 \dontrun{
+# Compare to the version without transforming rate parameters
 fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
-summary(fit.2, data=FALSE)
+fit.2.s <- summary(fit.2)
+print(fit.2.s$par, 3)
+print(fit.2.s$bpar, 3)
 }
 
 initials <- fit$start$value
@@ -88,7 +94,9 @@ SFO_SFO.ff <- mkinmod(
   use_of_ff = "max")
 
 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff, data = FALSE)
+fit.ff.s <- summary(fit.ff)
+print(fit.ff.s$par, 3)
+print(fit.ff.s$bpar, 3)
 initials <- c("f_parent_to_m1" = 0.5)
 transformed <- transform_odeparms(initials, SFO_SFO.ff)
 backtransform_odeparms(transformed, SFO_SFO.ff)
@@ -101,7 +109,9 @@ SFO_SFO.ff.2 <- mkinmod(
 
 
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff.2, data = FALSE)
+fit.ff.2.s <- summary(fit.ff.2)
+print(fit.ff.2.s$par, 3)
+print(fit.ff.2.s$bpar, 3)
 }
 }
 \keyword{ manip }
-- 
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