Improve examples for showing with pkgdown

- Use quiet= TRUE in dontrun sections
- Use mkinsub in model definitions
- Avoid \code{\link{}} in titles

13 files changed, 72 insertions, 43 deletions

diff --git a/man/Extract.mmkin.Rd b/man/Extract.mmkin.Rd
index 6e0c84e3..e27e83a0 100644
--- a/man/Extract.mmkin.Rd
+++ b/man/Extract.mmkin.Rd
@@ -31,8 +31,15 @@
                 cores = 1, quiet = TRUE)
   fits["FOMC", ]
   fits[, "B"]
-  fits[, "B", drop = TRUE]$FOMC
   fits["SFO", "B"]
-  fits[["SFO", "B"]] # This is equivalent to
-  fits["SFO", "B", drop = TRUE]
+
+  head(
+    # 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/endpoints.Rd b/man/endpoints.Rd
index 08773c3e..55a4cb0a 100644
--- a/man/endpoints.Rd
+++ b/man/endpoints.Rd
@@ -23,6 +23,10 @@ endpoints(fit)
 \value{
   A list with the components mentioned above.
 }
+\examples{
+  fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+  endpoints(fit)  
+}
 \author{
   Johannes Ranke
 }
diff --git a/man/mccall81_245T.Rd b/man/mccall81_245T.Rd
index 7cc5c363..656ca33f 100644
--- a/man/mccall81_245T.Rd
+++ b/man/mccall81_245T.Rd
@@ -32,10 +32,11 @@
                          phenol = list(type = "SFO", to = "anisole"),

                          anisole = list(type = "SFO"))

   \dontrun{

-    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"))

+    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)

     summary(fit.1, data = FALSE)

   }

-  # No covariance matrix and k_phenol_sink is really small, therefore fix it to zero

+  # 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)

diff --git a/man/mkinerrmin.Rd b/man/mkinerrmin.Rd
index 12c9ebd4..9229fc7f 100644
--- a/man/mkinerrmin.Rd
+++ b/man/mkinerrmin.Rd
@@ -4,9 +4,8 @@
 Calculate the minimum error to assume in order to pass the variance test

 }

 \description{

-This function uses \code{\link{optimize}} in order to iteratively find the

-smallest relative error still resulting in passing the chi-squared test

-as defined in the FOCUS kinetics report from 2006.

+This function finds the smallest relative error still resulting in passing the

+chi-squared test as defined in the FOCUS kinetics report from 2006.

 }

 \usage{

 mkinerrmin(fit, alpha = 0.05)

@@ -34,8 +33,8 @@ mkinerrmin(fit, alpha = 0.05)
     This function is used internally by \code{\link{summary.mkinfit}}.

 }

 \examples{

-SFO_SFO = mkinmod(parent = list(type = "SFO", to = "m1"),

-                  m1 = list(type = "SFO"),

+SFO_SFO = mkinmod(parent = mkinsub("SFO", to = "m1"),

+                  m1 = mkinsub("SFO"),

                   use_of_ff = "max")

 

 fit_FOCUS_D = mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

diff --git a/man/mkinfit.Rd b/man/mkinfit.Rd
index aa38b462..8e2fbeb1 100644
--- a/man/mkinfit.Rd
+++ b/man/mkinfit.Rd
@@ -275,10 +275,10 @@ FOMC_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
   m1 = mkinsub("SFO"))
 # Fit the model to the FOCUS example dataset D using defaults
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D)
+fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE)
 # Use starting parameters from parent only FOMC fit
-fit.FOMC = mkinfit("FOMC", FOCUS_2006_D)
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D,
+fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE)
+fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE,
   parms.ini = fit.FOMC$bparms.ode)
 
 # Use stepwise fitting, using optimised parameters from parent only fit, SFORB
@@ -286,24 +286,26 @@ SFORB_SFO <- mkinmod(
   parent = list(type = "SFORB", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
 # Fit the model to the FOCUS example dataset D using defaults
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D)
-fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve")
+fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE)
+fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve",
+                                 quiet = TRUE)
 # Use starting parameters from parent only SFORB fit (not really needed in this case)
-fit.SFORB = mkinfit("SFORB", FOCUS_2006_D)
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode)
+fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE)
+fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
 }
 
 \dontrun{
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
-f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)
+f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(f.noweight)
-f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs")
+f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
 summary(f.irls)
-f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean")
+f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
 summary(f.w.mean)
-f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value")
+f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value", 
+                     quiet = TRUE)
 summary(f.w.value)
 }
 
@@ -312,9 +314,9 @@ summary(f.w.value)
 dw <- FOCUS_2006_D
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
-f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man")
+f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
 summary(f.w.man)
-f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man",
+f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
                        reweight.method = "obs")
 summary(f.w.man.irls)
 }
diff --git a/man/mkinparplot.Rd b/man/mkinparplot.Rd
index 3eda08d2..34b06963 100644
--- a/man/mkinparplot.Rd
+++ b/man/mkinparplot.Rd
@@ -1,8 +1,7 @@
 \name{mkinparplot}

 \alias{mkinparplot}

 \title{

-  Function to plot the confidence intervals obtained using

-  \code{\link{mkinfit}}

+  Function to plot the confidence intervals obtained using mkinfit

 }

 \description{

   This function plots the confidence intervals for the parameters

@@ -25,9 +24,9 @@
 

 \examples{

 model <- mkinmod(

-  T245 = list(type = "SFO", to = c("phenol"), sink = FALSE),

-  phenol = list(type = "SFO", to = c("anisole")),

-  anisole = list(type = "SFO"), use_of_ff = "max")

+  T245 = mkinsub("SFO", to = c("phenol"), sink = FALSE),

+  phenol = mkinsub("SFO", to = c("anisole")),

+  anisole = mkinsub("SFO"), use_of_ff = "max")

 fit <- mkinfit(model, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)

 mkinparplot(fit)

 }

diff --git a/man/mmkin.Rd b/man/mmkin.Rd
index 3a8d4a1f..eb6d05eb 100644
--- a/man/mmkin.Rd
+++ b/man/mmkin.Rd
@@ -57,21 +57,22 @@ 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))
+time_default <- system.time(fits.0 <- mmkin(models, datasets, quiet = TRUE))
+time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE))
 
 time_default
 time_1
 
-endpoints(fits[["SFO_lin", 2]])
+endpoints(fits.0[["SFO_lin", 2]])
 
-# Plot.mkinfit handles rows or columns of mmkin result objects
+# plot.mkinfit handles rows or columns of mmkin result objects
 plot(fits.0[1, ])
 plot(fits.0[1, ], obs_var = c("M1", "M2"))
 plot(fits.0[, 1])
 # Use double brackets to extract a single mkinfit object, which will be plotted
-# by plot.mkinfit
+# by plot.mkinfit and can be plotted using plot_sep
 plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)
+plot_sep(fits.0[[1, 1]])
 # Plotting with mmkin (single brackets, extracting an mmkin object) does not
 # allow to plot the observed variables separately
 plot(fits.0[1, 1])
diff --git a/man/plot.mmkin.Rd b/man/plot.mmkin.Rd
index 57f69c90..7f3460d3 100644
--- a/man/plot.mmkin.Rd
+++ b/man/plot.mmkin.Rd
@@ -46,13 +46,14 @@
 }
 \examples{
   # 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),
+  fits <- mmkin(c("FOMC", "HS"), 
+                list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), # named list for titles
                 cores = 1, quiet = TRUE, method.modFit = "Marq")
   plot(fits[, "FOCUS C"])
   plot(fits["FOMC", ])
 
-  # We can also plot a single fit, if we like the way mmkin works, but then the plot
+  # We can also plot a single fit, if we like the way plot.mmkin works, but then the plot
   # height should be smaller than the plot width (this is not possible for the html pages
-  # generated by staticdocs, as far as I know).
+  # generated by pkgdown, as far as I know).
   plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
 }
diff --git a/man/print.mkinmod.Rd b/man/print.mkinmod.Rd
index fa02c1cb..24555def 100644
--- a/man/print.mkinmod.Rd
+++ b/man/print.mkinmod.Rd
@@ -7,7 +7,7 @@
   Print mkinmod objects in a way that the user finds his way to get to its components.
 }
 \usage{
-\method{print}{mkinmod}(x, ...)
+  \method{print}{mkinmod}(x, ...)
 }
 \arguments{
   \item{x}{
@@ -17,3 +17,10 @@
     Not used.
   }
 }
+\examples{
+  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")
+    
+  print(m_synth_SFO_lin)
+}
diff --git a/man/schaefer07_complex_case.Rd b/man/schaefer07_complex_case.Rd
index c666d08b..50272f4e 100644
--- a/man/schaefer07_complex_case.Rd
+++ b/man/schaefer07_complex_case.Rd
@@ -36,6 +36,12 @@ model <- mkinmod(
   B1 = list(type = "SFO"),

   C1 = list(type = "SFO"),

   A2 = list(type = "SFO"), use_of_ff = "max")

-\dontrun{mkinfit(model, data)}

+  \dontrun{

+    fit <- mkinfit(model, data, quiet = TRUE)

+    plot(fit)

+    endpoints(fit)

+  }

+ # Compare with the results obtained in the original publication

+ print(schaefer07_complex_results)

 }

 \keyword{datasets}

diff --git a/man/summary.mkinfit.Rd b/man/summary.mkinfit.Rd
index af09e86a..876fc362 100644
--- a/man/summary.mkinfit.Rd
+++ b/man/summary.mkinfit.Rd
@@ -70,6 +70,6 @@
   Johannes Ranke

 }

 \examples{

-  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))

+  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))

 }

 \keyword{ utilities }

diff --git a/man/synthetic_data_for_UBA.Rd b/man/synthetic_data_for_UBA.Rd
index 468e3731..a9739d55 100644
--- a/man/synthetic_data_for_UBA.Rd
+++ b/man/synthetic_data_for_UBA.Rd
@@ -61,7 +61,9 @@ m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),
                             M1 = list(type = "SFO"),

                             M2 = list(type = "SFO"), use_of_ff = "max")

 

-mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data)

+fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, quiet = TRUE)

+plot_sep(fit)

+summary(fit)

 }

 }

 \keyword{datasets}

diff --git a/man/transform_odeparms.Rd b/man/transform_odeparms.Rd
index 71c179d7..a1ccdf26 100644
--- a/man/transform_odeparms.Rd
+++ b/man/transform_odeparms.Rd
@@ -69,7 +69,7 @@ fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
 
 \dontrun{
-fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE)
+fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
 summary(fit.2, data=FALSE)
 }
 
@@ -87,7 +87,7 @@ SFO_SFO.ff <- mkinmod(
   m1 = list(type = "SFO"),
   use_of_ff = "max")
 
-fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D)
+fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff, data = FALSE)
 initials <- c("f_parent_to_m1" = 0.5)
 transformed <- transform_odeparms(initials, SFO_SFO.ff)
@@ -100,7 +100,7 @@ SFO_SFO.ff.2 <- mkinmod(
   use_of_ff = "max")
 
 
-fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D)
+fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
 summary(fit.ff.2, data = FALSE)
 }
 }