From 524a8bba89b95840b4e9215c403947a8bb76d7b2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Nov 2020 16:05:10 +0100 Subject: Complete rebuild of static docs of dev version --- docs/dev/reference/summary.nlme.mmkin.html | 230 +++++++++++++++-------------- 1 file changed, 117 insertions(+), 113 deletions(-) (limited to 'docs/dev/reference/summary.nlme.mmkin.html') diff --git a/docs/dev/reference/summary.nlme.mmkin.html b/docs/dev/reference/summary.nlme.mmkin.html index d016796e..2aeadc46 100644 --- a/docs/dev/reference/summary.nlme.mmkin.html +++ b/docs/dev/reference/summary.nlme.mmkin.html @@ -239,7 +239,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

k_in_pop <- log(2) / dt50_sfo_in_pop set.seed(1234) k_in <- rlnorm(5, log(k_in_pop), 0.5) -SFO <- mkinmod(parent = mkinsub("SFO")) +SFO <- mkinmod(parent = mkinsub("SFO")) pred_sfo <- function(k) { mkinpredict(SFO, @@ -251,6 +251,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

ds_sfo_mean <- lapply(k_in, pred_sfo) names(ds_sfo_mean) <- paste("ds", 1:5) +set.seed(12345) ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) { add_err(ds, sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2), @@ -260,13 +261,14 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

# Evaluate using mmkin and nlme library(nlme) f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1) -f_nlme <- nlme(f_mmkin) -
#> Warning: Iteration 3, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
summary(f_nlme, data = TRUE) +
#> Warning: Optimisation did not converge: +#> iteration limit reached without convergence (10)
f_nlme <- nlme(f_mmkin) +
#> Warning: Iteration 1, LME step: nlminb() did not converge (code = 1). Do increase 'msMaxIter'!
summary(f_nlme, data = TRUE)
#> nlme version used for fitting: 3.1.150.1 #> mkin version used for pre-fitting: 0.9.50.4 #> R version used for fitting: 4.0.3 -#> Date of fit: Thu Nov 19 14:59:43 2020 -#> Date of summary: Thu Nov 19 14:59:43 2020 +#> Date of fit: Mon Nov 30 16:01:23 2020 +#> Date of summary: Mon Nov 30 16:01:23 2020 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -276,146 +278,148 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

#> #> Model predictions using solution type analytical #> -#> Fitted in 0.681 s using 5 iterations +#> Fitted in 0.996 s using 6 iterations #> #> Variance model: Two-component variance function #> #> Mean of starting values for individual parameters: #> parent_0 log_k_parent -#> 97.849556 -4.455036 +#> 101.568773 -4.454103 #> #> Fixed degradation parameter values: #> None #> #> Results: #> -#> AIC BIC logLik -#> 555.792 570.7908 -271.896 +#> AIC BIC logLik +#> 586.4159 603.9145 -286.2079 #> #> Optimised, transformed parameters with symmetric confidence intervals: -#> lower est. upper -#> parent_0 94.701 97.763 100.826 -#> log_k_parent -5.008 -4.462 -3.916 +#> lower est. upper +#> parent_0 99.360 101.593 103.825 +#> log_k_parent -4.979 -4.451 -3.924 #> #> Correlation: #> prnt_0 -#> log_k_parent 0.024 +#> log_k_parent 0.155 #> #> Random effects: #> Formula: list(parent_0 ~ 1, log_k_parent ~ 1) #> Level: ds -#> Structure: Diagonal -#> parent_0 log_k_parent Residual -#> StdDev: 2.898 0.6119 1 +#> Structure: General positive-definite, Log-Cholesky parametrization +#> StdDev Corr +#> parent_0 0.2624248 prnt_0 +#> log_k_parent 0.5907146 0.999 +#> Residual 1.0000000 #> #> Variance function: #> Structure: Constant plus proportion of variance covariate #> Formula: ~fitted(.) #> Parameter estimates: -#> const prop -#> 1.55075176 0.05680853 +#> const prop +#> 6.56706e-24 7.89583e-02 #> #> Backtransformed parameters with asymmetric confidence intervals: -#> lower est. upper -#> parent_0 94.701336 97.76345 100.82556 -#> k_parent 0.006687 0.01154 0.01992 +#> lower est. upper +#> parent_0 99.360213 101.59280 103.82539 +#> k_parent 0.006883 0.01166 0.01976 #> #> Estimated disappearance times: #> DT50 DT90 -#> parent 60.05 199.5 +#> parent 59.44 197.4 #> #> Data: -#> ds name time observed predicted residual std standardized -#> ds 1 parent 0 103.6 97.42 6.17540 5.748 1.074413 -#> ds 1 parent 0 95.9 97.42 -1.52460 5.748 -0.265253 -#> ds 1 parent 1 95.4 96.72 -1.31719 5.709 -0.230721 -#> ds 1 parent 1 95.3 96.72 -1.41719 5.709 -0.248237 -#> ds 1 parent 3 91.6 95.32 -3.71774 5.633 -0.660046 -#> ds 1 parent 3 94.5 95.32 -0.81774 5.633 -0.145181 -#> ds 1 parent 7 88.1 92.58 -4.47930 5.483 -0.816920 -#> ds 1 parent 7 89.6 92.58 -2.97930 5.483 -0.543355 -#> ds 1 parent 14 90.3 87.97 2.32502 5.233 0.444318 -#> ds 1 parent 14 96.0 87.97 8.02502 5.233 1.533602 -#> ds 1 parent 28 80.2 79.44 0.75809 4.772 0.158862 -#> ds 1 parent 28 77.9 79.44 -1.54191 4.772 -0.323118 -#> ds 1 parent 60 59.3 62.92 -3.61742 3.896 -0.928458 -#> ds 1 parent 60 59.6 62.92 -3.31742 3.896 -0.851459 -#> ds 1 parent 90 59.4 50.56 8.83825 3.264 2.707613 -#> ds 1 parent 90 51.0 50.56 0.43825 3.264 0.134260 -#> ds 1 parent 120 38.8 40.63 -1.83247 2.781 -0.658968 -#> ds 1 parent 120 38.9 40.63 -1.73247 2.781 -0.623007 -#> ds 2 parent 0 103.2 97.17 6.02995 5.734 1.051655 -#> ds 2 parent 0 95.1 97.17 -2.07005 5.734 -0.361027 -#> ds 2 parent 1 88.3 95.59 -7.28901 5.647 -1.290694 -#> ds 2 parent 1 102.4 95.59 6.81099 5.647 1.206048 -#> ds 2 parent 3 88.4 92.50 -4.10371 5.479 -0.748984 -#> ds 2 parent 3 95.2 92.50 2.69629 5.479 0.492110 -#> ds 2 parent 7 83.5 86.63 -3.12863 5.160 -0.606349 -#> ds 2 parent 7 96.4 86.63 9.77137 5.160 1.893751 -#> ds 2 parent 14 77.3 77.23 0.06920 4.653 0.014871 -#> ds 2 parent 14 76.0 77.23 -1.23080 4.653 -0.264497 -#> ds 2 parent 28 61.7 61.38 0.31692 3.816 0.083043 -#> ds 2 parent 28 56.5 61.38 -4.88308 3.816 -1.279513 -#> ds 2 parent 60 35.1 36.31 -1.21343 2.581 -0.470178 -#> ds 2 parent 60 32.2 36.31 -4.11343 2.581 -1.593868 -#> ds 2 parent 90 21.2 22.20 -0.99906 1.999 -0.499832 -#> ds 2 parent 90 23.3 22.20 1.10094 1.999 0.550800 -#> ds 2 parent 120 14.1 13.57 0.52931 1.732 0.305638 -#> ds 2 parent 120 16.9 13.57 3.32931 1.732 1.922443 -#> ds 3 parent 0 92.4 94.12 -1.71979 5.567 -0.308917 -#> ds 3 parent 0 94.0 94.12 -0.11979 5.567 -0.021517 -#> ds 3 parent 1 95.7 91.97 3.72634 5.450 0.683712 -#> ds 3 parent 1 90.8 91.97 -1.17366 5.450 -0.215343 -#> ds 3 parent 3 86.7 87.83 -1.12709 5.225 -0.215720 -#> ds 3 parent 3 85.8 87.83 -2.02709 5.225 -0.387976 -#> ds 3 parent 7 77.1 80.09 -2.98635 4.807 -0.621300 -#> ds 3 parent 7 81.5 80.09 1.41365 4.807 0.294104 -#> ds 3 parent 14 69.1 68.15 0.95467 4.170 0.228922 -#> ds 3 parent 14 62.4 68.15 -5.74533 4.170 -1.377682 -#> ds 3 parent 28 49.1 49.34 -0.23911 3.203 -0.074644 -#> ds 3 parent 28 47.2 49.34 -2.13911 3.203 -0.667787 -#> ds 3 parent 60 21.9 23.58 -1.68477 2.049 -0.822090 -#> ds 3 parent 60 23.6 23.58 0.01523 2.049 0.007431 -#> ds 3 parent 90 12.4 11.81 0.59388 1.690 0.351500 -#> ds 3 parent 90 13.8 11.81 1.99388 1.690 1.180112 -#> ds 3 parent 120 4.9 5.91 -1.00993 1.587 -0.636506 -#> ds 3 parent 120 7.5 5.91 1.59007 1.587 1.002137 -#> ds 4 parent 0 91.8 101.72 -9.92097 5.983 -1.658171 -#> ds 4 parent 0 104.6 101.72 2.87903 5.983 0.481194 -#> ds 4 parent 1 117.5 101.27 16.23017 5.958 2.723944 -#> ds 4 parent 1 99.3 101.27 -1.96983 5.958 -0.330602 -#> ds 4 parent 3 94.0 100.37 -6.37355 5.909 -1.078583 -#> ds 4 parent 3 98.7 100.37 -1.67355 5.909 -0.283212 -#> ds 4 parent 7 109.2 98.60 10.59529 5.812 1.822915 -#> ds 4 parent 7 89.2 98.60 -9.40471 5.812 -1.618075 -#> ds 4 parent 14 103.3 95.58 7.71609 5.647 1.366386 -#> ds 4 parent 14 103.0 95.58 7.41609 5.647 1.313261 -#> ds 4 parent 28 90.8 89.82 0.98290 5.333 0.184310 -#> ds 4 parent 28 88.7 89.82 -1.11710 5.333 -0.209477 -#> ds 4 parent 60 74.8 77.91 -3.10870 4.690 -0.662879 -#> ds 4 parent 60 75.3 77.91 -2.60870 4.690 -0.556262 -#> ds 4 parent 90 71.1 68.18 2.91738 4.172 0.699234 -#> ds 4 parent 90 78.0 68.18 9.81738 4.172 2.353017 -#> ds 4 parent 120 59.1 59.67 -0.57073 3.728 -0.153107 -#> ds 4 parent 120 53.8 59.67 -5.87073 3.728 -1.574902 -#> ds 5 parent 0 94.9 98.38 -3.48183 5.800 -0.600307 -#> ds 5 parent 0 101.8 98.38 3.41817 5.800 0.589332 -#> ds 5 parent 1 96.1 96.75 -0.65141 5.711 -0.114065 -#> ds 5 parent 1 97.1 96.75 0.34859 5.711 0.061040 -#> ds 5 parent 3 93.8 93.57 0.22881 5.537 0.041323 -#> ds 5 parent 3 85.8 93.57 -7.77119 5.537 -1.403444 -#> ds 5 parent 7 87.6 87.52 0.07909 5.208 0.015186 -#> ds 5 parent 7 94.0 87.52 6.47909 5.208 1.244026 -#> ds 5 parent 14 82.5 77.86 4.64101 4.687 0.990182 -#> ds 5 parent 14 81.7 77.86 3.84101 4.687 0.819498 -#> ds 5 parent 28 60.0 61.62 -1.61729 3.829 -0.422433 -#> ds 5 parent 28 61.0 61.62 -0.61729 3.829 -0.161236 -#> ds 5 parent 60 32.5 36.10 -3.59608 2.571 -1.398750 -#> ds 5 parent 60 35.5 36.10 -0.59608 2.571 -0.231854 -#> ds 5 parent 90 21.8 21.86 -0.06415 1.987 -0.032287 -#> ds 5 parent 90 24.4 21.86 2.53585 1.987 1.276317 -#> ds 5 parent 120 14.1 13.24 0.85643 1.724 0.496877 -#> ds 5 parent 120 12.1 13.24 -1.14357 1.724 -0.663473
+#> ds name time observed predicted residual std standardized +#> ds 1 parent 0 104.1 101.417 2.68283 8.0077 0.335030 +#> ds 1 parent 0 105.0 101.417 3.58283 8.0077 0.447422 +#> ds 1 parent 1 98.5 100.624 -2.12400 7.9451 -0.267334 +#> ds 1 parent 1 96.1 100.624 -4.52400 7.9451 -0.569407 +#> ds 1 parent 3 101.9 99.056 2.84379 7.8213 0.363595 +#> ds 1 parent 3 85.2 99.056 -13.85621 7.8213 -1.771597 +#> ds 1 parent 7 99.1 95.994 3.10646 7.5795 0.409850 +#> ds 1 parent 7 93.0 95.994 -2.99354 7.5795 -0.394953 +#> ds 1 parent 14 88.1 90.860 -2.75997 7.1741 -0.384710 +#> ds 1 parent 14 84.1 90.860 -6.75997 7.1741 -0.942268 +#> ds 1 parent 28 80.2 81.402 -1.20174 6.4273 -0.186973 +#> ds 1 parent 28 91.3 81.402 9.89826 6.4273 1.540024 +#> ds 1 parent 60 65.1 63.316 1.78361 4.9994 0.356767 +#> ds 1 parent 60 65.8 63.316 2.48361 4.9994 0.496785 +#> ds 1 parent 90 47.8 50.029 -2.22862 3.9502 -0.564182 +#> ds 1 parent 90 53.5 50.029 3.47138 3.9502 0.878792 +#> ds 1 parent 120 37.6 39.529 -1.92946 3.1212 -0.618182 +#> ds 1 parent 120 39.3 39.529 -0.22946 3.1212 -0.073516 +#> ds 2 parent 0 107.9 101.711 6.18875 8.0309 0.770613 +#> ds 2 parent 0 102.1 101.711 0.38875 8.0309 0.048406 +#> ds 2 parent 1 103.8 100.174 3.62597 7.9096 0.458428 +#> ds 2 parent 1 108.6 100.174 8.42597 7.9096 1.065287 +#> ds 2 parent 3 91.0 97.169 -6.16895 7.6723 -0.804055 +#> ds 2 parent 3 84.9 97.169 -12.26895 7.6723 -1.599124 +#> ds 2 parent 7 79.3 91.427 -12.12652 7.2189 -1.679833 +#> ds 2 parent 7 100.9 91.427 9.47348 7.2189 1.312320 +#> ds 2 parent 14 77.3 82.182 -4.88174 6.4889 -0.752318 +#> ds 2 parent 14 83.5 82.182 1.31826 6.4889 0.203155 +#> ds 2 parent 28 66.8 66.402 0.39792 5.2430 0.075895 +#> ds 2 parent 28 63.3 66.402 -3.10208 5.2430 -0.591662 +#> ds 2 parent 60 40.8 40.789 0.01138 3.2206 0.003532 +#> ds 2 parent 60 44.8 40.789 4.01138 3.2206 1.245537 +#> ds 2 parent 90 27.8 25.830 1.97002 2.0395 0.965937 +#> ds 2 parent 90 27.0 25.830 1.17002 2.0395 0.573682 +#> ds 2 parent 120 15.2 16.357 -1.15721 1.2915 -0.895991 +#> ds 2 parent 120 15.5 16.357 -0.85721 1.2915 -0.663710 +#> ds 3 parent 0 97.7 101.907 -4.20726 8.0464 -0.522873 +#> ds 3 parent 0 88.2 101.907 -13.70726 8.0464 -1.703521 +#> ds 3 parent 1 109.9 99.522 10.37805 7.8581 1.320685 +#> ds 3 parent 1 97.8 99.522 -1.72195 7.8581 -0.219130 +#> ds 3 parent 3 100.5 94.918 5.58248 7.4945 0.744875 +#> ds 3 parent 3 77.4 94.918 -17.51752 7.4945 -2.337375 +#> ds 3 parent 7 78.3 86.338 -8.03788 6.8171 -1.179077 +#> ds 3 parent 7 90.3 86.338 3.96212 6.8171 0.581204 +#> ds 3 parent 14 76.0 73.147 2.85281 5.7756 0.493944 +#> ds 3 parent 14 79.1 73.147 5.95281 5.7756 1.030687 +#> ds 3 parent 28 46.0 52.504 -6.50373 4.1456 -1.568826 +#> ds 3 parent 28 53.4 52.504 0.89627 4.1456 0.216197 +#> ds 3 parent 60 25.1 24.605 0.49461 1.9428 0.254586 +#> ds 3 parent 60 21.4 24.605 -3.20539 1.9428 -1.649882 +#> ds 3 parent 90 11.0 12.090 -1.09046 0.9546 -1.142271 +#> ds 3 parent 90 14.2 12.090 2.10954 0.9546 2.209770 +#> ds 3 parent 120 5.8 5.941 -0.14094 0.4691 -0.300464 +#> ds 3 parent 120 6.1 5.941 0.15906 0.4691 0.339077 +#> ds 4 parent 0 95.3 101.177 -5.87672 7.9887 -0.735625 +#> ds 4 parent 0 102.0 101.177 0.82328 7.9887 0.103056 +#> ds 4 parent 1 104.4 100.716 3.68438 7.9523 0.463307 +#> ds 4 parent 1 105.4 100.716 4.68438 7.9523 0.589057 +#> ds 4 parent 3 113.7 99.800 13.90026 7.8800 1.763989 +#> ds 4 parent 3 82.3 99.800 -17.49974 7.8800 -2.220774 +#> ds 4 parent 7 98.1 97.993 0.10713 7.7374 0.013846 +#> ds 4 parent 7 87.8 97.993 -10.19287 7.7374 -1.317359 +#> ds 4 parent 14 97.9 94.909 2.99079 7.4939 0.399098 +#> ds 4 parent 14 104.8 94.909 9.89079 7.4939 1.319851 +#> ds 4 parent 28 85.0 89.030 -4.02995 7.0297 -0.573279 +#> ds 4 parent 28 77.2 89.030 -11.82995 7.0297 -1.682864 +#> ds 4 parent 60 82.2 76.923 5.27690 6.0737 0.868808 +#> ds 4 parent 60 86.1 76.923 9.17690 6.0737 1.510919 +#> ds 4 parent 90 70.5 67.073 3.42743 5.2959 0.647182 +#> ds 4 parent 90 61.7 67.073 -5.37257 5.2959 -1.014470 +#> ds 4 parent 120 60.0 58.483 1.51654 4.6178 0.328416 +#> ds 4 parent 120 56.4 58.483 -2.08346 4.6178 -0.451184 +#> ds 5 parent 0 92.6 101.752 -9.15161 8.0341 -1.139091 +#> ds 5 parent 0 116.5 101.752 14.74839 8.0341 1.835716 +#> ds 5 parent 1 108.0 100.069 7.93112 7.9013 1.003778 +#> ds 5 parent 1 104.9 100.069 4.83112 7.9013 0.611436 +#> ds 5 parent 3 100.5 96.786 3.71355 7.6421 0.485934 +#> ds 5 parent 3 89.5 96.786 -7.28645 7.6421 -0.953462 +#> ds 5 parent 7 91.7 90.541 1.15895 7.1490 0.162114 +#> ds 5 parent 7 95.1 90.541 4.55895 7.1490 0.637707 +#> ds 5 parent 14 82.2 80.566 1.63437 6.3613 0.256923 +#> ds 5 parent 14 84.5 80.566 3.93437 6.3613 0.618483 +#> ds 5 parent 28 60.5 63.791 -3.29084 5.0368 -0.653357 +#> ds 5 parent 28 72.8 63.791 9.00916 5.0368 1.788662 +#> ds 5 parent 60 38.3 37.412 0.88840 2.9540 0.300748 +#> ds 5 parent 60 40.7 37.412 3.28840 2.9540 1.113217 +#> ds 5 parent 90 22.5 22.685 -0.18500 1.7912 -0.103287 +#> ds 5 parent 90 20.8 22.685 -1.88500 1.7912 -1.052387 +#> ds 5 parent 120 13.4 13.755 -0.35534 1.0861 -0.327173 +#> ds 5 parent 120 13.8 13.755 0.04466 1.0861 0.041118