Add a nlme method for mmkin row objects

1 files changed, 6 insertions, 9 deletions

diff --git a/man/nlme.Rd b/man/nlme.Rd
index 8e5c2aa0..971ba3f5 100644
--- a/man/nlme.Rd
+++ b/man/nlme.Rd
@@ -101,14 +101,19 @@ plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))
   nlme_f_sfo_sfo <- nlme_function(f_2["SFO-SFO", ])
   nlme_f_sfo_sfo_ff <- nlme_function(f_2["SFO-SFO-ff", ])
   nlme_f_fomc_sfo <- nlme_function(f_2["FOMC-SFO", ])
+  assign("nlme_f_sfo_sfo", nlme_f_sfo_sfo, globalenv())
+  assign("nlme_f_sfo_sfo_ff", nlme_f_sfo_sfo_ff, globalenv())
+  assign("nlme_f_fomc_sfo", nlme_f_fomc_sfo, globalenv())
 
-  # Allowing for correlations between random effects leads to non-convergence
+  # Allowing for correlations between random effects (not shown)
+  # leads to non-convergence
   f_nlme_sfo_sfo <- nlme(value ~ nlme_f_sfo_sfo(name, time,
        parent_0, log_k_parent_sink, log_k_parent_A1, log_k_A1_sink),
      data = grouped_data_2,
      fixed = parent_0 + log_k_parent_sink + log_k_parent_A1 + log_k_A1_sink ~ 1,
      random = pdDiag(parent_0 + log_k_parent_sink + log_k_parent_A1 + log_k_A1_sink ~ 1),
      start = mean_dp_sfo_sfo)
+   # augPred does not see to work on this object, so no plot is shown
 
   # The same model fitted with transformed formation fractions does not converge
   f_nlme_sfo_sfo_ff <- nlme(value ~ nlme_f_sfo_sfo_ff(name, time,
@@ -118,14 +123,6 @@ plot(augPred(m_nlme, level = 0:1), layout = c(3, 1))
      random = pdDiag(parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1),
      start = mean_dp_sfo_sfo_ff)
 
-  # It does converge with this version of reduced random effects
-  f_nlme_sfo_sfo_ff <- nlme(value ~ nlme_f_sfo_sfo_ff(name, time,
-       parent_0, log_k_parent, log_k_A1, f_parent_ilr_1),
-     data = grouped_data_2,
-     fixed = parent_0 + log_k_parent + log_k_A1 + f_parent_ilr_1 ~ 1,
-     random = pdDiag(parent_0 + log_k_parent ~ 1),
-     start = mean_dp_sfo_sfo_ff)
-
   f_nlme_fomc_sfo <- nlme(value ~ nlme_f_fomc_sfo(name, time,
        parent_0, log_alpha, log_beta, log_k_A1, f_parent_ilr_1),
      data = grouped_data_2,