From a9427a09abdf7ce9aaeae7c7190f90c8f2e5ef52 Mon Sep 17 00:00:00 2001
From: Johannes Ranke
Date: Mon, 15 Feb 2021 14:08:13 +0100
Subject: Improve README, introductory vignette and some other docs
Also bump version to 1.0.3.
---
docs/reference/summary.nlme.mmkin.html | 80 +++++++++++++++++-----------------
1 file changed, 40 insertions(+), 40 deletions(-)
(limited to 'docs/reference/summary.nlme.mmkin.html')
diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html
index bc60b53e..d6840425 100644
--- a/docs/reference/summary.nlme.mmkin.html
+++ b/docs/reference/summary.nlme.mmkin.html
@@ -76,7 +76,7 @@ endpoints such as formation fractions and DT50 values. Optionally
mkin
- 1.0.0
+ 1.0.3
@@ -264,11 +264,11 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#> Warning: Optimisation did not converge:
#> iteration limit reached without convergence (10)
#> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
#> nlme version used for fitting: 3.1.151
-#> mkin version used for pre-fitting: 1.0.0
+
#> nlme version used for fitting: 3.1.152
+#> mkin version used for pre-fitting: 1.0.3
#> R version used for fitting: 4.0.3
-#> Date of fit: Wed Feb 3 17:32:05 2021
-#> Date of summary: Wed Feb 3 17:32:05 2021
+#> Date of fit: Mon Feb 15 13:46:13 2021
+#> Date of summary: Mon Feb 15 13:46:13 2021
#>
#> Equations:
#> d_parent/dt = - k_parent * parent
@@ -278,7 +278,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#>
#> Model predictions using solution type analytical
#>
-#> Fitted in 0.526 s using 4 iterations
+#> Fitted in 0.553 s using 4 iterations
#>
#> Variance model: Two-component variance function
#>
@@ -307,19 +307,19 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#> Formula: list(parent_0 ~ 1, log_k_parent ~ 1)
#> Level: ds
#> Structure: Diagonal
-#> parent_0 log_k_parent Residual
-#> StdDev: 6.91e-05 0.5863 1
+#> parent_0 log_k_parent Residual
+#> StdDev: 6.924e-05 0.5863 1
#>
#> Variance function:
#> Structure: Constant plus proportion of variance covariate
#> Formula: ~fitted(.)
#> Parameter estimates:
#> const prop
-#> 0.0001206605 0.0789967776
+#> 0.0001208853 0.0789968036
#>
#> Backtransformed parameters with asymmetric confidence intervals:
#> lower est. upper
-#> parent_0 99.370883 101.59243 103.81398
+#> parent_0 99.370882 101.59243 103.81398
#> k_parent 0.006923 0.01168 0.01972
#>
#> Estimated disappearance times:
@@ -330,68 +330,68 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#> ds name time observed predicted residual std standardized
#> ds 1 parent 0 104.1 101.592 2.50757 8.0255 0.312451
#> ds 1 parent 0 105.0 101.592 3.40757 8.0255 0.424594
-#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288314
+#> ds 1 parent 1 98.5 100.796 -2.29571 7.9625 -0.288313
#> ds 1 parent 1 96.1 100.796 -4.69571 7.9625 -0.589725
#> ds 1 parent 3 101.9 99.221 2.67904 7.8381 0.341796
-#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788813
+#> ds 1 parent 3 85.2 99.221 -14.02096 7.8381 -1.788812
#> ds 1 parent 7 99.1 96.145 2.95512 7.5951 0.389081
#> ds 1 parent 7 93.0 96.145 -3.14488 7.5951 -0.414065
-#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401988
+#> ds 1 parent 14 88.1 90.989 -2.88944 7.1879 -0.401987
#> ds 1 parent 14 84.1 90.989 -6.88944 7.1879 -0.958480
#> ds 1 parent 28 80.2 81.493 -1.29305 6.4377 -0.200857
-#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523365
+#> ds 1 parent 28 91.3 81.493 9.80695 6.4377 1.523364
#> ds 1 parent 60 65.1 63.344 1.75642 5.0039 0.351008
#> ds 1 parent 60 65.8 63.344 2.45642 5.0039 0.490898
-#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561253
+#> ds 1 parent 90 47.8 50.018 -2.21764 3.9512 -0.561252
#> ds 1 parent 90 53.5 50.018 3.48236 3.9512 0.881335
#> ds 1 parent 120 37.6 39.495 -1.89515 3.1200 -0.607423
#> ds 1 parent 120 39.3 39.495 -0.19515 3.1200 -0.062549
-#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785944
+#> ds 2 parent 0 107.9 101.592 6.30757 8.0255 0.785943
#> ds 2 parent 0 102.1 101.592 0.50757 8.0255 0.063245
-#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473362
-#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080627
+#> ds 2 parent 1 103.8 100.058 3.74159 7.9043 0.473361
+#> ds 2 parent 1 108.6 100.058 8.54159 7.9043 1.080626
#> ds 2 parent 3 91.0 97.060 -6.05952 7.6674 -0.790297
#> ds 2 parent 3 84.9 97.060 -12.15952 7.6674 -1.585874
-#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667252
-#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326648
+#> ds 2 parent 7 79.3 91.329 -12.02867 7.2147 -1.667251
+#> ds 2 parent 7 100.9 91.329 9.57133 7.2147 1.326647
#> ds 2 parent 14 77.3 82.102 -4.80185 6.4858 -0.740366
#> ds 2 parent 14 83.5 82.102 1.39815 6.4858 0.215571
#> ds 2 parent 28 66.8 66.351 0.44945 5.2415 0.085748
#> ds 2 parent 28 63.3 66.351 -3.05055 5.2415 -0.582002
#> ds 2 parent 60 40.8 40.775 0.02474 3.2211 0.007679
-#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249486
+#> ds 2 parent 60 44.8 40.775 4.02474 3.2211 1.249485
#> ds 2 parent 90 27.8 25.832 1.96762 2.0407 0.964198
#> ds 2 parent 90 27.0 25.832 1.16762 2.0407 0.572171
-#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901596
+#> ds 2 parent 120 15.2 16.366 -1.16561 1.2928 -0.901595
#> ds 2 parent 120 15.5 16.366 -0.86561 1.2928 -0.669547
#> ds 3 parent 0 97.7 101.592 -3.89243 8.0255 -0.485009
-#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668740
-#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362859
+#> ds 3 parent 0 88.2 101.592 -13.39243 8.0255 -1.668739
+#> ds 3 parent 1 109.9 99.218 10.68196 7.8379 1.362858
#> ds 3 parent 1 97.8 99.218 -1.41804 7.8379 -0.180921
#> ds 3 parent 3 100.5 94.634 5.86555 7.4758 0.784603
#> ds 3 parent 3 77.4 94.634 -17.23445 7.4758 -2.305360
-#> ds 3 parent 7 78.3 86.093 -7.79273 6.8010 -1.145813
-#> ds 3 parent 7 90.3 86.093 4.20727 6.8010 0.618621
-#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527849
-#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065723
+#> ds 3 parent 7 78.3 86.093 -7.79273 6.8011 -1.145813
+#> ds 3 parent 7 90.3 86.093 4.20727 6.8011 0.618620
+#> ds 3 parent 14 76.0 72.958 3.04222 5.7634 0.527848
+#> ds 3 parent 14 79.1 72.958 6.14222 5.7634 1.065722
#> ds 3 parent 28 46.0 52.394 -6.39404 4.1390 -1.544842
#> ds 3 parent 28 53.4 52.394 1.00596 4.1390 0.243046
#> ds 3 parent 60 25.1 24.582 0.51786 1.9419 0.266676
-#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638665
-#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143200
-#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206777
+#> ds 3 parent 60 21.4 24.582 -3.18214 1.9419 -1.638664
+#> ds 3 parent 90 11.0 12.092 -1.09202 0.9552 -1.143199
+#> ds 3 parent 90 14.2 12.092 2.10798 0.9552 2.206776
#> ds 3 parent 120 5.8 5.948 -0.14810 0.4699 -0.315178
#> ds 3 parent 120 6.1 5.948 0.15190 0.4699 0.323282
#> ds 4 parent 0 95.3 101.592 -6.29243 8.0255 -0.784057
-#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050785
+#> ds 4 parent 0 102.0 101.592 0.40757 8.0255 0.050784
#> ds 4 parent 1 104.4 101.125 3.27549 7.9885 0.410025
#> ds 4 parent 1 105.4 101.125 4.27549 7.9885 0.535205
#> ds 4 parent 3 113.7 100.195 13.50487 7.9151 1.706218
-#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260887
+#> ds 4 parent 3 82.3 100.195 -17.89513 7.9151 -2.260886
#> ds 4 parent 7 98.1 98.362 -0.26190 7.7703 -0.033706
#> ds 4 parent 7 87.8 98.362 -10.56190 7.7703 -1.359270
#> ds 4 parent 14 97.9 95.234 2.66590 7.5232 0.354357
-#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271522
+#> ds 4 parent 14 104.8 95.234 9.56590 7.5232 1.271521
#> ds 4 parent 28 85.0 89.274 -4.27372 7.0523 -0.606001
#> ds 4 parent 28 77.2 89.274 -12.07372 7.0523 -1.712017
#> ds 4 parent 60 82.2 77.013 5.18661 6.0838 0.852526
@@ -400,18 +400,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
#> ds 4 parent 90 61.7 67.053 -5.35308 5.2970 -1.010591
#> ds 4 parent 120 60.0 58.381 1.61905 4.6119 0.351058
#> ds 4 parent 120 56.4 58.381 -1.98095 4.6119 -0.429530
-#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120486
+#> ds 5 parent 0 92.6 101.592 -8.99243 8.0255 -1.120485
#> ds 5 parent 0 116.5 101.592 14.90757 8.0255 1.857531
#> ds 5 parent 1 108.0 99.914 8.08560 7.8929 1.024413
-#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631656
+#> ds 5 parent 1 104.9 99.914 4.98560 7.8929 0.631655
#> ds 5 parent 3 100.5 96.641 3.85898 7.6343 0.505477
-#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935383
+#> ds 5 parent 3 89.5 96.641 -7.14102 7.6343 -0.935382
#> ds 5 parent 7 91.7 90.412 1.28752 7.1423 0.180267
-#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656305
-#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273296
+#> ds 5 parent 7 95.1 90.412 4.68752 7.1423 0.656304
+#> ds 5 parent 14 82.2 80.463 1.73715 6.3563 0.273295
#> ds 5 parent 14 84.5 80.463 4.03715 6.3563 0.635141
#> ds 5 parent 28 60.5 63.728 -3.22788 5.0343 -0.641178
-#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802063
+#> ds 5 parent 28 72.8 63.728 9.07212 5.0343 1.802062
#> ds 5 parent 60 38.3 37.399 0.90061 2.9544 0.304835
#> ds 5 parent 60 40.7 37.399 3.30061 2.9544 1.117174
#> ds 5 parent 90 22.5 22.692 -0.19165 1.7926 -0.106913
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