From f0ef23a7598e5d19648ae4edc2b74e0fba27a41c Mon Sep 17 00:00:00 2001
From: Johannes Ranke
+# +# The procedure is greatly simplified by the nlme.mmkin function +f_nlme <- nlme(f) +plot(f_nlme) +sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120) -m_SFO <- mkinmod(parent = mkinsub("SFO")) +m_SFO <- mkinmod(parent = mkinsub("SFO")) d_SFO_1 <- mkinpredict(m_SFO, c(k_parent = 0.1), c(parent = 98), sampling_times) @@ -215,7 +215,7 @@ nlme for the case of a single grouping variable ds. assign("nlme_f", nlme_f, globalenv()) assign("grouped_data", grouped_data, globalenv()) -library(nlme) +library(nlme) m_nlme <- nlme(value ~ nlme_f(name, time, parent_0, log_k_parent_sink), data = grouped_data, fixed = parent_0 + log_k_parent_sink ~ 1, @@ -224,35 +224,38 @@ nlme for the case of a single grouping variable ds. summary(m_nlme)#> Nonlinear mixed-effects model fit by maximum likelihood #> Model: value ~ nlme_f(name, time, parent_0, log_k_parent_sink) -#> Data: grouped_data +#> Data: grouped_data #> AIC BIC logLik -#> 252.7798 262.1358 -121.3899 +#> 300.6824 310.2426 -145.3412 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent_sink ~ 1) #> Level: ds #> Structure: Diagonal -#> parent_0 log_k_parent_sink Residual -#> StdDev: 0.0006768135 0.6800777 2.489397 +#> parent_0 log_k_parent_sink Residual +#> StdDev: 1.697361 0.6801209 3.666073 #> -#> Fixed effects: parent_0 + log_k_parent_sink ~ 1 -#> Value Std.Error DF t-value p-value -#> parent_0 101.74884 0.6456014 44 157.60321 0 -#> log_k_parent_sink -3.05575 0.4015811 44 -7.60929 0 +#> Fixed effects: parent_0 + log_k_parent_sink ~ 1 +#> Value Std.Error DF t-value p-value +#> parent_0 100.99378 1.3890416 46 72.70753 0 +#> log_k_parent_sink -3.07521 0.4018589 46 -7.65246 0 #> Correlation: #> prnt_0 -#> log_k_parent_sink 0.026 +#> log_k_parent_sink 0.027 #> #> Standardized Within-Group Residuals: #> Min Q1 Med Q3 Max -#> -2.1317488 -0.6878121 0.0828385 0.8592270 2.9529864 +#> -1.9942823 -0.5622565 0.1791579 0.7165038 2.0704781 #> -#> Number of Observations: 48 +#> Number of Observations: 50 #> Number of Groups: 3# augPred does not seem to work on fits with more than one state +# augPred does not work on fits with more than one state # variable - -