diff options
| author | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-14 17:22:00 +0200 |
|---|---|---|
| committer | Johannes Ranke <jranke@uni-bremen.de> | 2020-04-14 17:22:00 +0200 |
| commit | 26085403289e29259e500282e8e88a5ab00c07a0 (patch) | |
| tree | e86d5195c725ee0c08a45e4393ff9c1dfad64314 /R/nlme.R | |
| parent | d4a49b4837de347d34b2c198de7342c34b0fab63 (diff) | |
Add a nlme method for mmkin row objects
Diffstat (limited to 'R/nlme.R')
| -rw-r--r-- | R/nlme.R | 17 |
1 files changed, 7 insertions, 10 deletions
@@ -1,4 +1,4 @@ -#' Estimation of parameter distributions from mmkin row objects +#' Helper functions to create nlme models from mmkin row objects #' #' These functions facilitate setting up a nonlinear mixed effects model for #' an mmkin row object. An mmkin row object is essentially a list of mkinfit @@ -81,14 +81,19 @@ #' 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, @@ -98,14 +103,6 @@ #' 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, |