Documentation improvements, mainly fixing example code

The errors in the example code were in the \dontrun sections, so they
were not caught by CRAN checks. In addition, the static help files
generated with pkgdown were cached, so I noticed the errors only
after completely regenerating the documentation for version 1.0.0.

1 files changed, 19 insertions, 18 deletions

diff --git a/man/nlme.mmkin.Rd b/man/nlme.mmkin.Rd
index f78256ac..2fb0488a 100644
--- a/man/nlme.mmkin.Rd
+++ b/man/nlme.mmkin.Rd
@@ -79,6 +79,12 @@ This functions sets up a nonlinear mixed effects model for an mmkin row
 object. An mmkin row object is essentially a list of mkinfit objects that
 have been obtained by fitting the same model to a list of datasets.
 }
+\details{
+Note that the convergence of the nlme algorithms depends on the quality
+of the data. In degradation kinetics, we often only have few datasets
+(e.g. data for few soils) and complicated degradation models, which may
+make it impossible to obtain convergence with nlme.
+}
 \note{
 As the object inherits from \link[nlme:nlme]{nlme::nlme}, there is a wealth of
 methods that will automatically work on 'nlme.mmkin' objects, such as
@@ -120,11 +126,10 @@ f_nlme_sfo <- nlme(f["SFO", ])
   # f_nlme_sfo_sfo_ff <- nlme(f_2["SFO-SFO-ff", ])
   #plot(f_nlme_sfo_sfo_ff)
 
-  # With the log-Cholesky parameterization, this converges in 11
-  # iterations and around 100 seconds, but without tweaking control
-  # parameters (with pdDiag, increasing the tolerance and pnlsMaxIter was
-  # necessary)
-  f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ])
+  # For the following, we need to increase pnlsMaxIter and the tolerance
+  # to get convergence
+  f_nlme_dfop_sfo <- nlme(f_2["DFOP-SFO", ],
+    control = list(pnlsMaxIter = 120, tolerance = 5e-4))
 
   plot(f_nlme_dfop_sfo)
 
@@ -144,22 +149,18 @@ f_nlme_sfo <- nlme(f["SFO", ])
     print(f_nlme_dfop_tc)
   }
 
-  f_2_obs <- mmkin(list("SFO-SFO" = m_sfo_sfo,
-   "DFOP-SFO" = m_dfop_sfo),
-    ds_2, quiet = TRUE, error_model = "obs")
+  f_2_obs <- update(f_2, error_model = "obs")
   f_nlme_sfo_sfo_obs <- nlme(f_2_obs["SFO-SFO", ])
   print(f_nlme_sfo_sfo_obs)
-  f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ])
+  f_nlme_dfop_sfo_obs <- nlme(f_2_obs["DFOP-SFO", ],
+    control = list(pnlsMaxIter = 120, tolerance = 5e-4))
 
-  f_2_tc <- mmkin(list("SFO-SFO" = m_sfo_sfo,
-   "DFOP-SFO" = m_dfop_sfo),
-    ds_2, quiet = TRUE, error_model = "tc")
-  # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # stops with error message
-  f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ])
-  # We get warnings about false convergence in the LME step in several iterations
-  # but as the last such warning occurs in iteration 25 and we have 28 iterations
-  # we can ignore these
-  anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs, f_nlme_dfop_sfo_tc)
+  f_2_tc <- update(f_2, error_model = "tc")
+  # f_nlme_sfo_sfo_tc <- nlme(f_2_tc["SFO-SFO", ]) # No convergence with 50 iterations
+  # f_nlme_dfop_sfo_tc <- nlme(f_2_tc["DFOP-SFO", ],
+  #  control = list(pnlsMaxIter = 120, tolerance = 5e-4)) # Error in X[, fmap[[nm]]] <- gradnm
+
+  anova(f_nlme_dfop_sfo, f_nlme_dfop_sfo_obs)
 
 }
 }