From 9d6a975a0e3850a36889a18b5d9929d27b901ab3 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 4 Mar 2019 14:09:45 +0100 Subject: Make some example output more reproducible In order to avoid some unnecessary documentation rebuilds --- docs/articles/FOCUS_D.html | 6 +- docs/articles/FOCUS_L.html | 36 +-- docs/articles/web_only/NAFTA_examples.html | 14 +- docs/articles/web_only/compiled_models.html | 10 +- docs/reference/Extract.mmkin.html | 367 ---------------------------- docs/reference/NAFTA_SOP_2015.html | 6 +- docs/reference/mccall81_245T.html | 229 ++++------------- docs/reference/mkinfit.html | 44 ++-- docs/reference/mkinmod.html | 2 +- docs/reference/mkinpredict.html | 2 +- docs/reference/mmkin.html | 4 +- docs/reference/nafta.html | 6 +- docs/reference/summary.mkinfit.html | 6 +- docs/reference/transform_odeparms.html | 330 ++++--------------------- man/Extract.mmkin.Rd | 5 - man/mccall81_245T.Rd | 6 +- man/transform_odeparms.Rd | 18 +- 17 files changed, 177 insertions(+), 914 deletions(-) diff --git a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index fabb567a..376acee2 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -166,8 +166,8 @@ 
summary(fit)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:33 2019 
-## Date of summary: Mon Mar  4 10:09:33 2019 
+## Date of fit:     Mon Mar  4 14:06:39 2019 
+## Date of summary: Mon Mar  4 14:06:39 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -175,7 +175,7 @@
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.687 s
+## Fitted with method Port using 153 model solutions performed in 0.693 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/FOCUS_L.html b/docs/articles/FOCUS_L.html
index 7157f973..5dac9999 100644
--- a/docs/articles/FOCUS_L.html
+++ b/docs/articles/FOCUS_L.html
@@ -114,15 +114,15 @@
 summary(m.L1.SFO)
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:35 2019 
-## Date of summary: Mon Mar  4 10:09:35 2019 
+## Date of fit:     Mon Mar  4 14:06:41 2019 
+## Date of summary: Mon Mar  4 14:06:41 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.102 s
+## Fitted with method Port using 37 model solutions performed in 0.095 s
 ## 
 ## Weighting: none
 ## 
@@ -205,15 +205,15 @@
 
summary(m.L1.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:36 2019 
-## Date of summary: Mon Mar  4 10:09:36 2019 
+## Date of fit:     Mon Mar  4 14:06:43 2019 
+## Date of summary: Mon Mar  4 14:06:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 611 model solutions performed in 1.508 s
+## Fitted with method Port using 611 model solutions performed in 1.502 s
 ## 
 ## Weighting: none
 ## 
@@ -300,8 +300,8 @@
 
summary(m.L2.FOMC, data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:37 2019 
-## Date of summary: Mon Mar  4 10:09:37 2019 
+## Date of fit:     Mon Mar  4 14:06:43 2019 
+## Date of summary: Mon Mar  4 14:06:43 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
@@ -373,8 +373,8 @@
 ## covariance matrix; singular system.

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:38 2019 
-## Date of summary: Mon Mar  4 10:09:38 2019 
+## Date of fit:     Mon Mar  4 14:06:44 2019 
+## Date of summary: Mon Mar  4 14:06:44 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -383,7 +383,7 @@
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.841 s
+## Fitted with method Port using 336 model solutions performed in 0.84 s
 ## 
 ## Weighting: none
 ## 
@@ -463,8 +463,8 @@
 
summary(mm.L3[["DFOP", 1]])

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:39 2019 
-## Date of summary: Mon Mar  4 10:09:39 2019 
+## Date of fit:     Mon Mar  4 14:06:45 2019 
+## Date of summary: Mon Mar  4 14:06:46 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) *
@@ -564,8 +564,8 @@
 
summary(mm.L4[["SFO", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:40 2019 
-## Date of summary: Mon Mar  4 10:09:40 2019 
+## Date of fit:     Mon Mar  4 14:06:46 2019 
+## Date of summary: Mon Mar  4 14:06:46 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - k_parent_sink * parent
@@ -624,15 +624,15 @@
 
summary(mm.L4[["FOMC", 1]], data = FALSE)

 
## mkin version used for fitting:    0.9.48.1 
 ## R version used for fitting:       3.5.2 
-## Date of fit:     Mon Mar  4 10:09:40 2019 
-## Date of summary: Mon Mar  4 10:09:40 2019 
+## Date of fit:     Mon Mar  4 14:06:46 2019 
+## Date of summary: Mon Mar  4 14:06:46 2019 
 ## 
 ## Equations:
 ## d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.162 s
+## Fitted with method Port using 66 model solutions performed in 0.173 s
 ## 
 ## Weighting: none
 ## 
diff --git a/docs/articles/web_only/NAFTA_examples.html b/docs/articles/web_only/NAFTA_examples.html
index db1fc478..12e5d522 100644
--- a/docs/articles/web_only/NAFTA_examples.html
+++ b/docs/articles/web_only/NAFTA_examples.html
@@ -347,7 +347,7 @@
 ##      DT50 DT90 DT50_rep
 ## SFO  86.3  287     86.3
 ## IORE 53.4  668    201.0
-## DFOP 55.6  517    253.5
+## DFOP 55.6  517    253.0
 ## 
 ## Representative half-life:
 ## [1] 201.0316

@@ -492,9 +492,9 @@
 ## 
 ## DTx values:
 ##      DT50 DT90 DT50_rep
-## SFO  14.0 46.5    13.99
+## SFO  14.0 46.5    14.00
 ## IORE 16.4 29.4     8.86
-## DFOP 14.0 46.5    13.99
+## DFOP 14.0 46.5    14.00
 ## 
 ## Representative half-life:
 ## [1] 8.862193

@@ -644,9 +644,9 @@
 ## 
 ## DTx values:
 ##      DT50 DT90 DT50_rep
-## SFO  11.8 39.1    11.76
+## SFO  11.8 39.1    11.80
 ## IORE 12.9 31.4     9.46
-## DFOP 11.8 39.1    11.76
+## DFOP 11.8 39.1    11.80
 ## 
 ## Representative half-life:
 ## [1] 9.461912

@@ -830,9 +830,9 @@
 ## 
 ## DTx values:
 ##      DT50 DT90 DT50_rep
-## SFO   143  474    142.7
+## SFO   143  474    143.0
 ## IORE  131  236     71.2
-## DFOP  143  474    142.7
+## DFOP  143  474    143.0
 ## 
 ## Representative half-life:
 ## [1] 71.18014

diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html
index 1d96ea76..269b1098 100644
--- a/docs/articles/web_only/compiled_models.html
+++ b/docs/articles/web_only/compiled_models.html
@@ -129,9 +129,9 @@
 }

 
## Lade nötiges Paket: rbenchmark

 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   2.313    1.000     2.312        0
-## 1 deSolve, not compiled            3  17.602    7.610    17.595        0
-## 2      Eigenvalue based            3   2.853    1.233     2.851        0
+## 3     deSolve, compiled            3   2.310    1.000     2.308        0
+## 1 deSolve, not compiled            3  17.509    7.580    17.500        0
+## 2      Eigenvalue based            3   2.859    1.238     2.858        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -160,8 +160,8 @@
 }

 
## Successfully compiled differential equation model from auto-generated C code.

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.049    1.000     4.047        0
-## 1 deSolve, not compiled            3  37.135    9.171    37.119        0
+## 2     deSolve, compiled            3   4.074    1.000     4.072        0
+## 1 deSolve, not compiled            3  37.219    9.136    37.203        0
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html
index 96b9f218..3567af48 100644
--- a/docs/reference/Extract.mmkin.html
+++ b/docs/reference/Extract.mmkin.html
@@ -206,373 +206,6 @@
 #> 
 #> $counts
 #> [1] "relative convergence (4)"
-#> 

-  head(
-  # The same can be achieved by
-    fits["SFO", "B", drop = TRUE]
-  )
#> [[1]]
-#> $par
-#>          parent_0 log_k_parent_sink 
-#>         99.174072         -2.549028 
-#> 
-#> $ssr
-#> [1] 30.65564
-#> 
-#> $convergence
-#> [1] 0
-#> 
-#> $iterations
-#> [1] 5
-#> 
-#> $evaluations
-#> function gradient 
-#>        8       15 
-#> 
-#> $counts
-#> [1] "relative convergence (4)"
-#> 
-#> $hessian
-#>                     parent_0 log_k_parent_sink
-#> parent_0            4.163631         -94.09343
-#> log_k_parent_sink -94.093431        6311.34610
-#> 
-#> $residuals
-#>      parent      parent      parent      parent      parent      parent 
-#>  0.55407218 -2.98452128  4.20445742 -1.68599939 -0.58185357 -0.72033730 
-#>      parent      parent 
-#> -0.24260405 -0.07020339 
-#> 
-#> $ms
-#> [1] 3.831956
-#> 
-#> $var_ms
-#>   parent 
-#> 3.831956 
-#> 
-#> $var_ms_unscaled
-#>   parent 
-#> 3.831956 
-#> 
-#> $var_ms_unweighted
-#>   parent 
-#> 3.831956 
-#> 
-#> $rank
-#> [1] 2
-#> 
-#> $df.residual
-#> [1] 6
-#> 
-#> $solution_type
-#> [1] "analytical"
-#> 
-#> $transform_rates
-#> [1] TRUE
-#> 
-#> $transform_fractions
-#> [1] TRUE
-#> 
-#> $method.modFit
-#> [1] "Port"
-#> 
-#> $maxit.modFit
-#> [1] "auto"
-#> 
-#> $calls
-#> [1] 29
-#> 
-#> $time
-#>        User      System verstrichen 
-#>       0.069       0.000       0.069 
-#> 
-#> $mkinmod
-#> <mkinmod> model generated with
-#> Use of formation fractions $use_of_ff: min 
-#> Specification $spec:
-#> $parent
-#> $type: SFO; $sink: TRUE
-#> Coefficient matrix $coefmat available
-#> Differential equations:
-#> d_parent/dt = - k_parent_sink * parent
-#> 
-#> $observed
-#>     name time value
-#> 1 parent    0 98.62
-#> 2 parent    3 81.43
-#> 3 parent    7 53.18
-#> 4 parent   14 34.89
-#> 5 parent   30 10.09
-#> 6 parent   62  1.50
-#> 7 parent   90  0.33
-#> 8 parent  118  0.08
-#> 
-#> $obs_vars
-#> [1] "parent"
-#> 
-#> $predicted
-#>       name       time       value
-#> 1   parent   0.000000 99.17407218
-#> 2   parent   1.191919 90.35253561
-#> 3   parent   2.383838 82.31567498
-#> 4   parent   3.000000 78.44547872
-#> 5   parent   3.575758 74.99369333
-#> 6   parent   4.767677 68.32300215
-#> 7   parent   5.959596 62.24566915
-#> 8   parent   7.000000 57.38445742
-#> 9   parent   7.151515 56.70891509
-#> 10  parent   8.343434 51.66465547
-#> 11  parent   9.535354 47.06908288
-#> 12  parent  10.727273 42.88228661
-#> 13  parent  11.919192 39.06790599
-#> 14  parent  13.111111 35.59281463
-#> 15  parent  14.000000 33.20400061
-#> 16  parent  14.303030 32.42683275
-#> 17  parent  15.494949 29.54246504
-#> 18  parent  16.686869 26.91466193
-#> 19  parent  17.878788 24.52060198
-#> 20  parent  19.070707 22.33949373
-#> 21  parent  20.262626 20.35239512
-#> 22  parent  21.454545 18.54204899
-#> 23  parent  22.646465 16.89273320
-#> 24  parent  23.838384 15.39012410
-#> 25  parent  25.030303 14.02117212
-#> 26  parent  26.222222 12.77398846
-#> 27  parent  27.414141 11.63774182
-#> 28  parent  28.606061 10.60256435
-#> 29  parent  29.797980  9.65946594
-#> 30  parent  30.000000  9.50814643
-#> 31  parent  30.989899  8.80025617
-#> 32  parent  32.181818  8.01747313
-#> 33  parent  33.373737  7.30431867
-#> 34  parent  34.565657  6.65459931
-#> 35  parent  35.757576  6.06267251
-#> 36  parent  36.949495  5.52339762
-#> 37  parent  38.141414  5.03209124
-#> 38  parent  39.333333  4.58448658
-#> 39  parent  40.525253  4.17669637
-#> 40  parent  41.717172  3.80517911
-#> 41  parent  42.909091  3.46670832
-#> 42  parent  44.101010  3.15834451
-#> 43  parent  45.292929  2.87740968
-#> 44  parent  46.484848  2.62146400
-#> 45  parent  47.676768  2.38828471
-#> 46  parent  48.868687  2.17584671
-#> 47  parent  50.060606  1.98230508
-#> 48  parent  51.252525  1.80597899
-#> 49  parent  52.444444  1.64533711
-#> 50  parent  53.636364  1.49898432
-#> 51  parent  54.828283  1.36564963
-#> 52  parent  56.020202  1.24417505
-#> 53  parent  57.212121  1.13350565
-#> 54  parent  58.404040  1.03268029
-#> 55  parent  59.595960  0.94082335
-#> 56  parent  60.787879  0.85713708
-#> 57  parent  61.979798  0.78089471
-#> 58  parent  62.000000  0.77966270
-#> 59  parent  63.171717  0.71143411
-#> 60  parent  64.363636  0.64815202
-#> 61  parent  65.555556  0.59049888
-#> 62  parent  66.747475  0.53797399
-#> 63  parent  67.939394  0.49012119
-#> 64  parent  69.131313  0.44652489
-#> 65  parent  70.323232  0.40680649
-#> 66  parent  71.515152  0.37062104
-#> 67  parent  72.707071  0.33765429
-#> 68  parent  73.898990  0.30761993
-#> 69  parent  75.090909  0.28025713
-#> 70  parent  76.282828  0.25532825
-#> 71  parent  77.474747  0.23261679
-#> 72  parent  78.666667  0.21192552
-#> 73  parent  79.858586  0.19307474
-#> 74  parent  81.050505  0.17590074
-#> 75  parent  82.242424  0.16025436
-#> 76  parent  83.434343  0.14599973
-#> 77  parent  84.626263  0.13301305
-#> 78  parent  85.818182  0.12118154
-#> 79  parent  87.010101  0.11040244
-#> 80  parent  88.202020  0.10058214
-#> 81  parent  89.393939  0.09163535
-#> 82  parent  90.000000  0.08739595
-#> 83  parent  90.585859  0.08348439
-#> 84  parent  91.777778  0.07605845
-#> 85  parent  92.969697  0.06929305
-#> 86  parent  94.161616  0.06312943
-#> 87  parent  95.353535  0.05751406
-#> 88  parent  96.545455  0.05239819
-#> 89  parent  97.737374  0.04773737
-#> 90  parent  98.929293  0.04349113
-#> 91  parent 100.121212  0.03962259
-#> 92  parent 101.313131  0.03609816
-#> 93  parent 102.505051  0.03288723
-#> 94  parent 103.696970  0.02996191
-#> 95  parent 104.888889  0.02729679
-#> 96  parent 106.080808  0.02486874
-#> 97  parent 107.272727  0.02265667
-#> 98  parent 108.464646  0.02064136
-#> 99  parent 109.656566  0.01880531
-#> 100 parent 110.848485  0.01713257
-#> 101 parent 112.040404  0.01560863
-#> 102 parent 113.232323  0.01422024
-#> 103 parent 114.424242  0.01295535
-#> 104 parent 115.616162  0.01180297
-#> 105 parent 116.808081  0.01075310
-#> 106 parent 118.000000  0.00979661
-#> 
-#> $cost
-#> function (P) 
-#> {
-#>     assign("calls", calls + 1, inherits = TRUE)
-#>     if (trace_parms) 
-#>         cat(P, "\n")
-#>     if (length(state.ini.optim) > 0) {
-#>         odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#>         names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#>     }
-#>     else {
-#>         odeini <- state.ini.fixed
-#>         names(odeini) <- state.ini.fixed.boxnames
-#>     }
-#>     odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-#>         transparms.fixed)
-#>     parms <- backtransform_odeparms(odeparms, mkinmod, transform_rates = transform_rates, 
-#>         transform_fractions = transform_fractions)
-#>     out <- mkinpredict(mkinmod, parms, odeini, outtimes, solution_type = solution_type, 
-#>         use_compiled = use_compiled, method.ode = method.ode, 
-#>         atol = atol, rtol = rtol, ...)
-#>     assign("out_predicted", out, inherits = TRUE)
-#>     mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-#>         scaleVar = scaleVar)
-#>     if (mC$model < cost.old) {
-#>         if (!quiet) 
-#>             cat("Model cost at call ", calls, ": ", mC$model, 
-#>                 "\n")
-#>         if (plot) {
-#>             outtimes_plot = seq(min(observed$time), max(observed$time), 
-#>                 length.out = 100)
-#>             out_plot <- mkinpredict(mkinmod, parms, odeini, outtimes_plot, 
-#>                 solution_type = solution_type, use_compiled = use_compiled, 
-#>                 method.ode = method.ode, atol = atol, rtol = rtol, 
-#>                 ...)
-#>             plot(0, type = "n", xlim = range(observed$time), 
-#>                 ylim = c(0, max(observed$value, na.rm = TRUE)), 
-#>                 xlab = "Time", ylab = "Observed")
-#>             col_obs <- pch_obs <- 1:length(obs_vars)
-#>             lty_obs <- rep(1, length(obs_vars))
-#>             names(col_obs) <- names(pch_obs) <- names(lty_obs) <- obs_vars
-#>             for (obs_var in obs_vars) {
-#>                 points(subset(observed, name == obs_var, c(time, 
-#>                   value)), pch = pch_obs[obs_var], col = col_obs[obs_var])
-#>             }
-#>             matlines(out_plot$time, out_plot[-1], col = col_obs, 
-#>                 lty = lty_obs)
-#>             legend("topright", inset = c(0.05, 0.05), legend = obs_vars, 
-#>                 col = col_obs, pch = pch_obs, lty = 1:length(pch_obs))
-#>         }
-#>         assign("cost.old", mC$model, inherits = TRUE)
-#>     }
-#>     return(mC)
-#> }
-#> <bytecode: 0x55555c1f3208>
-#> <environment: 0x555555c27dc0>
-#> 
-#> $cost_notrans
-#> function (P) 
-#> {
-#>     if (length(state.ini.optim) > 0) {
-#>         odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed)
-#>         names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames)
-#>     }
-#>     else {
-#>         odeini <- state.ini.fixed
-#>         names(odeini) <- state.ini.fixed.boxnames
-#>     }
-#>     odeparms <- c(P[(length(state.ini.optim) + 1):length(P)], 
-#>         parms.fixed)
-#>     out <- mkinpredict(mkinmod, odeparms, odeini, outtimes, solution_type = solution_type, 
-#>         use_compiled = use_compiled, method.ode = method.ode, 
-#>         atol = atol, rtol = rtol, ...)
-#>     mC <- modCost(out, observed, y = "value", err = err, weight = weight, 
-#>         scaleVar = scaleVar)
-#>     return(mC)
-#> }
-#> <bytecode: 0x55555b84fce8>
-#> <environment: 0x555555c27dc0>
-#> 
-#> $hessian_notrans
-#>                   parent_0 k_parent_sink
-#> parent_0          4.163631     -1203.894
-#> k_parent_sink -1203.893702   1033188.753
-#> 
-#> $start
-#>               value   type
-#> parent_0      98.62  state
-#> k_parent_sink  0.10 deparm
-#> 
-#> $start_transformed
-#>                       value lower upper
-#> parent_0          98.620000  -Inf   Inf
-#> log_k_parent_sink -2.302585  -Inf   Inf
-#> 
-#> $fixed
-#> [1] value type 
-#> <0 Zeilen> (oder row.names mit Länge 0)
-#> 
-#> $data
-#>   time variable observed   predicted    residual
-#> 1    0   parent    98.62 99.17407218 -0.55407218
-#> 2    3   parent    81.43 78.44547872  2.98452128
-#> 3    7   parent    53.18 57.38445742 -4.20445742
-#> 4   14   parent    34.89 33.20400061  1.68599939
-#> 5   30   parent    10.09  9.50814643  0.58185357
-#> 6   62   parent     1.50  0.77966270  0.72033730
-#> 7   90   parent     0.33  0.08739595  0.24260405
-#> 8  118   parent     0.08  0.00979661  0.07020339
-#> 
-#> $atol
-#> [1] 1e-08
-#> 
-#> $rtol
-#> [1] 1e-10
-#> 
-#> $weight.ini
-#> [1] "none"
-#> 
-#> $tc.ini
-#> sigma_low  rsd_high 
-#>      0.50      0.07 
-#> 
-#> $reweight.tol
-#> [1] 1e-08
-#> 
-#> $reweight.max.iter
-#> [1] 10
-#> 
-#> $bparms.optim
-#>      parent_0 k_parent_sink 
-#>   99.17407218    0.07815759 
-#> 
-#> $bparms.fixed
-#> numeric(0)
-#> 
-#> $bparms.ode
-#> k_parent_sink 
-#>    0.07815759 
-#> 
-#> $bparms.state
-#>   parent 
-#> 99.17407 
-#> 
-#> $date
-#> [1] "Mon Mar  4 10:07:37 2019"
-#> 
-#> $version
-#> [1] "0.9.48.1"
-#> 
-#> $Rversion
-#> [1] "3.5.2"
-#> 
-#> attr(,"class")
-#> [1] "mkinfit" "modFit" 
 #>
plot(nafta_evaluation)
diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 5fbbc962..47fa6482 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -161,189 +161,60 @@ 
  SFO_SFO_SFO <- mkinmod(T245 = list(type = "SFO", to = "phenol"),
                          phenol = list(type = "SFO", to = "anisole"),
                          anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
  
    fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE)
-    summary(fit.1, data = FALSE)
#> Warning: Could not estimate covariance matrix; singular system.
#> mkin version used for fitting:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:08:00 2019 
-#> Date of summary: Mon Mar  4 10:08:00 2019 
-#> 
-#> Equations:
-#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
-#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
-#>            k_phenol_anisole * phenol
-#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
-#> 
-#> Model predictions using solution type deSolve 
-#> 
-#> Fitted with method Port using 574 model solutions performed in 3.762 s
-#> 
-#> Weighting: none
-#> 
-#> Starting values for parameters to be optimised:
-#>                     value   type
-#> T245_0           100.9000  state
-#> k_T245_sink        0.1000 deparm
-#> k_T245_phenol      0.1001 deparm
-#> k_phenol_sink      0.1002 deparm
-#> k_phenol_anisole   0.1003 deparm
-#> k_anisole_sink     0.1004 deparm
-#> 
-#> Starting values for the transformed parameters actually optimised:
-#>                           value lower upper
-#> T245_0               100.900000  -Inf   Inf
-#> log_k_T245_sink       -2.302585  -Inf   Inf
-#> log_k_T245_phenol     -2.301586  -Inf   Inf
-#> log_k_phenol_sink     -2.300587  -Inf   Inf
-#> log_k_phenol_anisole  -2.299590  -Inf   Inf
-#> log_k_anisole_sink    -2.298593  -Inf   Inf
-#> 
-#> Fixed parameter values:
-#>           value  type
-#> phenol_0      0 state
-#> anisole_0     0 state
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>                      Estimate Std. Error Lower Upper
-#> T245_0               103.9000         NA    NA    NA
-#> log_k_T245_sink       -4.1130         NA    NA    NA
-#> log_k_T245_phenol     -3.6120         NA    NA    NA
-#> log_k_phenol_sink    -25.0800         NA    NA    NA
-#> log_k_phenol_anisole  -0.9037         NA    NA    NA
-#> log_k_anisole_sink    -5.0090         NA    NA    NA
-#> 
-#> Parameter correlation:
-#> Could not estimate covariance matrix; singular system.
-#> Residual standard error: 2.78 on 18 degrees of freedom
-#> 
-#> Backtransformed parameters:
-#> Confidence intervals for internally transformed parameters are asymmetric.
-#> t-test (unrealistically) based on the assumption of normal distribution
-#> for estimators of untransformed parameters.
-#>                   Estimate   t value    Pr(>t) Lower Upper
-#> T245_0           1.039e+02 4.282e+01 7.236e-20    NA    NA
-#> k_T245_sink      1.636e-02 8.901e-01 1.926e-01    NA    NA
-#> k_T245_phenol    2.701e-02 1.504e+00 7.498e-02    NA    NA
-#> k_phenol_sink    1.286e-11 4.575e-11 5.000e-01    NA    NA
-#> k_phenol_anisole 4.051e-01 2.518e+00 1.075e-02    NA    NA
-#> k_anisole_sink   6.679e-03 8.146e+00 9.469e-08    NA    NA
-#> 
-#> Chi2 error levels in percent:
-#>          err.min n.optim df
-#> All data  10.070       6 16
-#> T245       7.908       3  5
-#> phenol   106.445       2  5
-#> anisole    5.379       1  6
-#> 
-#> Resulting formation fractions:
-#>                       ff
-#> T245_sink      3.772e-01
-#> T245_phenol    6.228e-01
-#> phenol_sink    3.175e-11
-#> phenol_anisole 1.000e+00
-#> anisole_sink   1.000e+00
-#> 
-#> Estimated disappearance times:
-#>            DT50    DT90
-#> T245     15.982  53.091
-#> phenol    1.711   5.685
-#> anisole 103.784 344.763
    # No convergence, no covariance matrix ...
+    summary(fit.1)$bpar
#> Warning: Could not estimate covariance matrix; singular system.
#>                      Estimate   se_notrans      t value       Pr(>t) Lower
+#> T245_0           1.038550e+02 2.4256088519 4.281607e+01 7.235908e-20    NA
+#> k_T245_sink      1.636106e-02 0.0183803090 8.901408e-01 1.925667e-01    NA
+#> k_T245_phenol    2.700936e-02 0.0179604385 1.503825e+00 7.498498e-02    NA
+#> k_phenol_sink    1.286034e-11 0.2810970202 4.575054e-11 5.000000e-01    NA
+#> k_phenol_anisole 4.050581e-01 0.1608928349 2.517564e+00 1.075371e-02    NA
+#> k_anisole_sink   6.678742e-03 0.0008199239 8.145563e+00 9.469402e-08    NA
+#>                  Upper
+#> T245_0              NA
+#> k_T245_sink         NA
+#> k_T245_phenol       NA
+#> k_phenol_sink       NA
+#> k_phenol_anisole    NA
+#> k_anisole_sink      NA
    endpoints(fit.1)
#> $ff
+#>      T245_sink    T245_phenol    phenol_sink phenol_anisole   anisole_sink 
+#>   3.772401e-01   6.227599e-01   3.174937e-11   1.000000e+00   1.000000e+00 
+#> 
+#> $SFORB
+#> logical(0)
+#> 
+#> $distimes
+#>               DT50      DT90
+#> T245     15.982025  53.09114
+#> phenol    1.711229   5.68458
+#> anisole 103.784093 344.76330
+#> 
    # No convergence, no covariance matrix ...
     # k_phenol_sink is really small, therefore fix it to zero
     fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"),
                    parms.ini = c(k_phenol_sink = 0),
                    fixed_parms = "k_phenol_sink", quiet = TRUE)
-    summary(fit.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:08:02 2019 
-#> Date of summary: Mon Mar  4 10:08:02 2019 
-#> 
-#> Equations:
-#> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245
-#> d_phenol/dt = + k_T245_phenol * T245 - k_phenol_sink * phenol -
-#>            k_phenol_anisole * phenol
-#> d_anisole/dt = + k_phenol_anisole * phenol - k_anisole_sink * anisole
-#> 
-#> Model predictions using solution type deSolve 
-#> 
-#> Fitted with method Port using 246 model solutions performed in 1.598 s
-#> 
-#> Weighting: none
-#> 
-#> Starting values for parameters to be optimised:
-#>                     value   type
-#> T245_0           100.9000  state
-#> k_T245_sink        0.1000 deparm
-#> k_T245_phenol      0.1001 deparm
-#> k_phenol_anisole   0.1002 deparm
-#> k_anisole_sink     0.1003 deparm
-#> 
-#> Starting values for the transformed parameters actually optimised:
-#>                           value lower upper
-#> T245_0               100.900000  -Inf   Inf
-#> log_k_T245_sink       -2.302585  -Inf   Inf
-#> log_k_T245_phenol     -2.301586  -Inf   Inf
-#> log_k_phenol_anisole  -2.300587  -Inf   Inf
-#> log_k_anisole_sink    -2.299590  -Inf   Inf
-#> 
-#> Fixed parameter values:
-#>               value   type
-#> phenol_0          0  state
-#> anisole_0         0  state
-#> k_phenol_sink     0 deparm
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>                      Estimate Std. Error  Lower    Upper
-#> T245_0               103.9000    2.35200 98.930 108.8000
-#> log_k_T245_sink       -4.1130    0.13250 -4.390  -3.8350
-#> log_k_T245_phenol     -3.6120    0.05002 -3.716  -3.5070
-#> log_k_phenol_anisole  -0.9037    0.30580 -1.544  -0.2637
-#> log_k_anisole_sink    -5.0090    0.11180 -5.243  -4.7750
-#> 
-#> Parameter correlation:
-#>                        T245_0 log_k_T245_sink log_k_T245_phenol
-#> T245_0                1.00000         0.63761           -0.1742
-#> log_k_T245_sink       0.63761         1.00000           -0.3831
-#> log_k_T245_phenol    -0.17416        -0.38313            1.0000
-#> log_k_phenol_anisole -0.05948         0.08745           -0.3047
-#> log_k_anisole_sink   -0.16208        -0.60469            0.5227
-#>                      log_k_phenol_anisole log_k_anisole_sink
-#> T245_0                           -0.05948            -0.1621
-#> log_k_T245_sink                   0.08745            -0.6047
-#> log_k_T245_phenol                -0.30470             0.5227
-#> log_k_phenol_anisole              1.00000            -0.1774
-#> log_k_anisole_sink               -0.17744             1.0000
-#> 
-#> Residual standard error: 2.706 on 19 degrees of freedom
-#> 
-#> Backtransformed parameters:
-#> Confidence intervals for internally transformed parameters are asymmetric.
-#> t-test (unrealistically) based on the assumption of normal distribution
-#> for estimators of untransformed parameters.
-#>                   Estimate t value    Pr(>t)     Lower     Upper
-#> T245_0           1.039e+02  44.160 6.462e-21 98.930000 108.80000
-#> k_T245_sink      1.636e-02   7.545 1.978e-07  0.012400   0.02159
-#> k_T245_phenol    2.701e-02  19.990 1.607e-14  0.024320   0.02999
-#> k_phenol_anisole 4.051e-01   3.270 2.014e-03  0.213600   0.76820
-#> k_anisole_sink   6.679e-03   8.942 1.544e-08  0.005285   0.00844
-#> 
-#> Chi2 error levels in percent:
-#>          err.min n.optim df
-#> All data   9.831       5 17
-#> T245       7.908       3  5
-#> phenol    99.808       1  6
-#> anisole    5.379       1  6
-#> 
-#> Resulting formation fractions:
-#>                    ff
-#> T245_sink      0.3772
-#> T245_phenol    0.6228
-#> phenol_anisole 1.0000
-#> phenol_sink    0.0000
-#> anisole_sink   1.0000
-#> 
-#> Estimated disappearance times:
-#>            DT50    DT90
-#> T245     15.982  53.091
-#> phenol    1.711   5.685
-#> anisole 103.784 344.763
+ summary(fit.2)$bpar
#> Estimate se_notrans t value Pr(>t) Lower +#> T245_0 1.038550e+02 2.3517950656 44.159900 6.461715e-21 98.932670927 +#> k_T245_sink 1.636106e-02 0.0021685502 7.544701 1.978480e-07 0.012397413 +#> k_T245_phenol 2.700936e-02 0.0013511301 19.990199 1.606634e-14 0.024324422 +#> k_phenol_anisole 4.050581e-01 0.1238660786 3.270129 2.013627e-03 0.213574853 +#> k_anisole_sink 6.678742e-03 0.0007468908 8.942059 1.543812e-08 0.005284957 +#> Upper +#> T245_0 1.087774e+02 +#> k_T245_sink 2.159195e-02 +#> k_T245_phenol 2.999066e-02 +#> k_phenol_anisole 7.682180e-01 +#> k_anisole_sink 8.440105e-03
endpoints(fit.1)
#> $ff +#> T245_sink T245_phenol phenol_sink phenol_anisole anisole_sink +#> 3.772401e-01 6.227599e-01 3.174937e-11 1.000000e+00 1.000000e+00 +#> +#> $SFORB +#> logical(0) +#> +#> $distimes +#> DT50 DT90 +#> T245 15.982025 53.09114 +#> phenol 1.711229 5.68458 +#> anisole 103.784093 344.76330 +#>
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:05 2019 -#> Date of summary: Mon Mar 4 10:08:05 2019 +#> Date of fit: Mon Mar 4 14:05:12 2019 +#> Date of summary: Mon Mar 4 14:05:12 2019 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -518,7 +518,7 @@ m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
#> User System verstrichen -#> 1.026 0.000 1.035
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.013 0.000 1.014
coef(fit)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
endpoints(fit)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -593,7 +593,7 @@ #> Model cost at call 146 : 371.2134 #> Optimisation by method Port successfully terminated. #> User System verstrichen -#> 0.814 0.008 0.830
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 0.821 0.000 0.822
coef(fit.deSolve)
#> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
endpoints(fit.deSolve)
#> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 @@ -631,8 +631,8 @@ m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE) summary(f.noweight)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:17 2019 -#> Date of summary: Mon Mar 4 10:08:17 2019 +#> Date of fit: Mon Mar 4 14:05:24 2019 +#> Date of summary: Mon Mar 4 14:05:24 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -640,7 +640,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 186 model solutions performed in 0.853 s +#> Fitted with method Port using 186 model solutions performed in 0.841 s #> #> Weighting: none #> @@ -748,8 +748,8 @@ #> 120 m1 33.31 28.78984 4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE) summary(f.irls)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:20 2019 -#> Date of summary: Mon Mar 4 10:08:20 2019 +#> Date of fit: Mon Mar 4 14:05:26 2019 +#> Date of summary: Mon Mar 4 14:05:26 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -757,7 +757,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 551 model solutions performed in 2.525 s +#> Fitted with method Port using 551 model solutions performed in 2.517 s #> #> Weighting: none #> @@ -870,8 +870,8 @@ #> 120 m1 33.31 28.80898 4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE) summary(f.w.mean)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:21 2019 -#> Date of summary: Mon Mar 4 10:08:21 2019 +#> Date of fit: Mon Mar 4 14:05:27 2019 +#> Date of summary: Mon Mar 4 14:05:27 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -879,7 +879,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 155 model solutions performed in 0.706 s +#> Fitted with method Port using 155 model solutions performed in 0.704 s #> #> Weighting: mean #> @@ -988,8 +988,8 @@ quiet = TRUE) summary(f.w.value)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:22 2019 -#> Date of summary: Mon Mar 4 10:08:22 2019 +#> Date of fit: Mon Mar 4 14:05:28 2019 +#> Date of summary: Mon Mar 4 14:05:28 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -997,7 +997,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 174 model solutions performed in 0.875 s +#> Fitted with method Port using 174 model solutions performed in 0.866 s #> #> Weighting: manual #> @@ -1108,8 +1108,8 @@ f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) summary(f.w.man)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:23 2019 -#> Date of summary: Mon Mar 4 10:08:23 2019 +#> Date of fit: Mon Mar 4 14:05:30 2019 +#> Date of summary: Mon Mar 4 14:05:30 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1117,7 +1117,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 270 model solutions performed in 1.279 s +#> Fitted with method Port using 270 model solutions performed in 1.23 s #> #> Weighting: manual #> @@ -1226,8 +1226,8 @@ reweight.method = "obs") summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.48.1 #> R version used for fitting: 3.5.2 -#> Date of fit: Mon Mar 4 10:08:26 2019 -#> Date of summary: Mon Mar 4 10:08:26 2019 +#> Date of fit: Mon Mar 4 14:05:33 2019 +#> Date of summary: Mon Mar 4 14:05:33 2019 #> #> Equations: #> d_parent/dt = - k_parent * parent @@ -1235,7 +1235,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 692 model solutions performed in 3.203 s +#> Fitted with method Port using 692 model solutions performed in 3.197 s #> #> Weighting: manual #> diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index ddb695e3..37f95690 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -234,7 +234,7 @@ For the definition of model types and their parameters, the equations given SFO_SFO <- mkinmod( parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument: -#> /usr/lib/R/bin/R CMD SHLIB file135d360177d0.c 2> file135d360177d0.c.err.txt +#> /usr/lib/R/bin/R CMD SHLIB filef43390002d2.c 2> filef43390002d2.c.err.txt #> Program source: #> 1: #include <R.h> #> 2: diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index a0880959..fb4afa9a 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -328,7 +328,7 @@ c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "eigen")[201,]))
#> time parent m1 #> 201 20 4.978707 27.46227
#> User System verstrichen -#> 0.004 0.000 0.004
system.time( +#> 0.004 0.000 0.003
system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), c(parent = 100, m1 = 0), seq(0, 20, by = 0.1), solution_type = "deSolve")[201,]))
#> time parent m1 diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5f82f41f..af963d13 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -194,8 +194,8 @@ time_1 <- system.time(fits.4 <- mmkin(models, datasets, cores = 1, quiet = TRUE)) time_default
#> User System verstrichen -#> 0.057 0.014 6.939
time_1
#> User System verstrichen -#> 22.525 0.000 22.538
+#> 0.049 0.025 6.950
time_1
#> User System verstrichen +#> 22.404 0.000 22.417
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340480 0.2659520 0.7505686 0.2494314 diff --git a/docs/reference/nafta.html b/docs/reference/nafta.html index 38e642df..f12e24e0 100644 --- a/docs/reference/nafta.html +++ b/docs/reference/nafta.html @@ -212,9 +212,9 @@ #> #> DTx values: #> DT50 DT90 DT50_rep -#> SFO 407 1352 407 -#> IORE 541 5192060 1562966 -#> DFOP 429 2383 841 +#> SFO 407 1350 407 +#> IORE 541 5190000 1560000 +#> DFOP 429 2380 841 #> #> Representative half-life: #> [1] 841.4096
plot(nafta_evaluation)
diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index e2f4d2e2..f561e258 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -211,15 +211,15 @@

Examples

  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version used for fitting:    0.9.48.1 
 #> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:09:19 2019 
-#> Date of summary: Mon Mar  4 10:09:19 2019 
+#> Date of fit:     Mon Mar  4 14:06:25 2019 
+#> Date of summary: Mon Mar  4 14:06:25 2019 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.086 s
+#> Fitted with method Port using 35 model solutions performed in 0.085 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index 3148f00b..fbc792f1 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -203,157 +203,29 @@ The transformation of sets of formation fractions is fragile, as it supposes
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version used for fitting:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:09:27 2019 
-#> Date of summary: Mon Mar  4 10:09:27 2019 
-#> 
-#> Equations:
-#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
-#> 
-#> Model predictions using solution type deSolve 
-#> 
-#> Fitted with method Port using 153 model solutions performed in 0.699 s
-#> 
-#> Weighting: none
-#> 
-#> Starting values for parameters to be optimised:
-#>                  value   type
-#> parent_0      100.7500  state
-#> k_parent_sink   0.1000 deparm
-#> k_parent_m1     0.1001 deparm
-#> k_m1_sink       0.1002 deparm
-#> 
-#> Starting values for the transformed parameters actually optimised:
-#>                        value lower upper
-#> parent_0          100.750000  -Inf   Inf
-#> log_k_parent_sink  -2.302585  -Inf   Inf
-#> log_k_parent_m1    -2.301586  -Inf   Inf
-#> log_k_m1_sink      -2.300587  -Inf   Inf
-#> 
-#> Fixed parameter values:
-#>      value  type
-#> m1_0     0 state
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>                   Estimate Std. Error  Lower   Upper
-#> parent_0            99.600    1.61400 96.330 102.900
-#> log_k_parent_sink   -3.038    0.07826 -3.197  -2.879
-#> log_k_parent_m1     -2.980    0.04124 -3.064  -2.897
-#> log_k_m1_sink       -5.248    0.13610 -5.523  -4.972
-#> 
-#> Parameter correlation:
-#>                   parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink
-#> parent_0           1.00000            0.6075        -0.06625       -0.1701
-#> log_k_parent_sink  0.60752            1.0000        -0.08740       -0.6253
-#> log_k_parent_m1   -0.06625           -0.0874         1.00000        0.4716
-#> log_k_m1_sink     -0.17006           -0.6253         0.47164        1.0000
-#> 
-#> Residual standard error: 3.211 on 36 degrees of freedom
-#> 
-#> Backtransformed parameters:
-#> Confidence intervals for internally transformed parameters are asymmetric.
-#> t-test (unrealistically) based on the assumption of normal distribution
-#> for estimators of untransformed parameters.
-#>                Estimate t value    Pr(>t)     Lower     Upper
-#> parent_0      99.600000  61.720 2.024e-38 96.330000 1.029e+02
-#> k_parent_sink  0.047920  12.780 3.050e-15  0.040890 5.616e-02
-#> k_parent_m1    0.050780  24.250 3.407e-24  0.046700 5.521e-02
-#> k_m1_sink      0.005261   7.349 5.758e-09  0.003992 6.933e-03
-#> 
-#> Chi2 error levels in percent:
-#>          err.min n.optim df
-#> All data   6.398       4 15
-#> parent     6.827       3  6
-#> m1         4.490       1  9
-#> 
-#> Resulting formation fractions:
-#>                 ff
-#> parent_sink 0.4855
-#> parent_m1   0.5145
-#> m1_sink     1.0000
-#> 
-#> Estimated disappearance times:
-#>           DT50   DT90
-#> parent   7.023  23.33
-#> m1     131.761 437.70

-
fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
-summary(fit.2, data=FALSE)
#> mkin version used for fitting:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:09:29 2019 
-#> Date of summary: Mon Mar  4 10:09:29 2019 
-#> 
-#> Equations:
-#> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
-#> d_m1/dt = + k_parent_m1 * parent - k_m1_sink * m1
-#> 
-#> Model predictions using solution type deSolve 
-#> 
-#> Fitted with method Port using 350 model solutions performed in 1.584 s
-#> 
-#> Weighting: none
-#> 
-#> Starting values for parameters to be optimised:
-#>                  value   type
-#> parent_0      100.7500  state
-#> k_parent_sink   0.1000 deparm
-#> k_parent_m1     0.1001 deparm
-#> k_m1_sink       0.1002 deparm
-#> 
-#> Starting values for the transformed parameters actually optimised:
-#>                  value lower upper
-#> parent_0      100.7500  -Inf   Inf
-#> k_parent_sink   0.1000     0   Inf
-#> k_parent_m1     0.1001     0   Inf
-#> k_m1_sink       0.1002     0   Inf
-#> 
-#> Fixed parameter values:
-#>      value  type
-#> m1_0     0 state
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>                Estimate Std. Error     Lower     Upper
-#> parent_0      99.600000  1.6140000 96.330000 1.029e+02
-#> k_parent_sink  0.047920  0.0037500  0.040310 5.553e-02
-#> k_parent_m1    0.050780  0.0020940  0.046530 5.502e-02
-#> k_m1_sink      0.005261  0.0007159  0.003809 6.713e-03
-#> 
-#> Parameter correlation:
-#>               parent_0 k_parent_sink k_parent_m1 k_m1_sink
-#> parent_0       1.00000        0.6075    -0.06625   -0.1701
-#> k_parent_sink  0.60752        1.0000    -0.08740   -0.6253
-#> k_parent_m1   -0.06625       -0.0874     1.00000    0.4716
-#> k_m1_sink     -0.17006       -0.6253     0.47164    1.0000
-#> 
-#> Residual standard error: 3.211 on 36 degrees of freedom
-#> 
-#> Backtransformed parameters:
-#> Confidence intervals for internally transformed parameters are asymmetric.
-#> t-test (unrealistically) based on the assumption of normal distribution
-#> for estimators of untransformed parameters.
-#>                Estimate t value    Pr(>t)     Lower     Upper
-#> parent_0      99.600000  61.720 2.024e-38 96.330000 1.029e+02
-#> k_parent_sink  0.047920  12.780 3.050e-15  0.040310 5.553e-02
-#> k_parent_m1    0.050780  24.250 3.407e-24  0.046530 5.502e-02
-#> k_m1_sink      0.005261   7.349 5.758e-09  0.003809 6.713e-03
-#> 
-#> Chi2 error levels in percent:
-#>          err.min n.optim df
-#> All data   6.398       4 15
-#> parent     6.827       3  6
-#> m1         4.490       1  9
-#> 
-#> Resulting formation fractions:
-#>                 ff
-#> parent_sink 0.4855
-#> parent_m1   0.5145
-#> m1_sink     1.0000
-#> 
-#> Estimated disappearance times:
-#>           DT50   DT90
-#> parent   7.023  23.33
-#> m1     131.761 437.70

+fit.s <- summary(fit)
+# Transformed and backtransformed parameters
+print(fit.s$par, 3)
#>                   Estimate Std. Error Lower  Upper
+#> parent_0             99.60     1.6137 96.33 102.87
+#> log_k_parent_sink    -3.04     0.0783 -3.20  -2.88
+#> log_k_parent_m1      -2.98     0.0412 -3.06  -2.90
+#> log_k_m1_sink        -5.25     0.1361 -5.52  -4.97
print(fit.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> parent_0      99.59848   1.613712   61.72 2.02e-38 96.32572 1.03e+02
+#> k_parent_sink  0.04792   0.003750   12.78 3.05e-15  0.04089 5.62e-02
+#> k_parent_m1    0.05078   0.002094   24.25 3.41e-24  0.04670 5.52e-02
+#> k_m1_sink      0.00526   0.000716    7.35 5.76e-09  0.00399 6.93e-03

+
# Compare to the version without transforming rate parameters
+fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
+fit.2.s <- summary(fit.2)
+print(fit.2.s$par, 3)
#>               Estimate Std. Error    Lower    Upper
+#> parent_0      99.59848   1.613710 96.32573 1.03e+02
+#> k_parent_sink  0.04792   0.003750  0.04031 5.55e-02
+#> k_parent_m1    0.05078   0.002094  0.04653 5.50e-02
+#> k_m1_sink      0.00526   0.000716  0.00381 6.71e-03
print(fit.2.s$bpar, 3)
#>               Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> parent_0      99.59848   1.613710   61.72 2.02e-38 96.32573 1.03e+02
+#> k_parent_sink  0.04792   0.003750   12.78 3.05e-15  0.04031 5.55e-02
+#> k_parent_m1    0.05078   0.002094   24.25 3.41e-24  0.04653 5.50e-02
+#> k_m1_sink      0.00526   0.000716    7.35 5.76e-09  0.00381 6.71e-03

 initials <- fit$start$value
 names(initials) <- rownames(fit$start)
 transformed <- fit$start_transformed$value
@@ -367,80 +239,16 @@ The transformation of sets of formation fractions is fragile, as it supposes
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:09:30 2019 
-#> Date of summary: Mon Mar  4 10:09:30 2019 
-#> 
-#> Equations:
-#> d_parent/dt = - k_parent * parent
-#> d_m1/dt = + f_parent_to_m1 * k_parent * parent - k_m1 * m1
-#> 
-#> Model predictions using solution type deSolve 
-#> 
-#> Fitted with method Port using 186 model solutions performed in 0.86 s
-#> 
-#> Weighting: none
-#> 
-#> Starting values for parameters to be optimised:
-#>                   value   type
-#> parent_0       100.7500  state
-#> k_parent         0.1000 deparm
-#> k_m1             0.1001 deparm
-#> f_parent_to_m1   0.5000 deparm
-#> 
-#> Starting values for the transformed parameters actually optimised:
-#>                     value lower upper
-#> parent_0       100.750000  -Inf   Inf
-#> log_k_parent    -2.302585  -Inf   Inf
-#> log_k_m1        -2.301586  -Inf   Inf
-#> f_parent_ilr_1   0.000000  -Inf   Inf
-#> 
-#> Fixed parameter values:
-#>      value  type
-#> m1_0     0 state
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>                Estimate Std. Error   Lower    Upper
-#> parent_0       99.60000    1.61400 96.3300 102.9000
-#> log_k_parent   -2.31600    0.04187 -2.4010  -2.2310
-#> log_k_m1       -5.24800    0.13610 -5.5230  -4.9720
-#> f_parent_ilr_1  0.04096    0.06477 -0.0904   0.1723
-#> 
-#> Parameter correlation:
-#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
-#> parent_0         1.0000       0.5178  -0.1701        -0.5489
-#> log_k_parent     0.5178       1.0000  -0.3285        -0.5451
-#> log_k_m1        -0.1701      -0.3285   1.0000         0.7466
-#> f_parent_ilr_1  -0.5489      -0.5451   0.7466         1.0000
-#> 
-#> Residual standard error: 3.211 on 36 degrees of freedom
-#> 
-#> Backtransformed parameters:
-#> Confidence intervals for internally transformed parameters are asymmetric.
-#> t-test (unrealistically) based on the assumption of normal distribution
-#> for estimators of untransformed parameters.
-#>                 Estimate t value    Pr(>t)     Lower     Upper
-#> parent_0       99.600000  61.720 2.024e-38 96.330000 1.029e+02
-#> k_parent        0.098700  23.880 5.700e-24  0.090660 1.074e-01
-#> k_m1            0.005261   7.349 5.758e-09  0.003992 6.933e-03
-#> f_parent_to_m1  0.514500  22.490 4.375e-23  0.468100 5.606e-01
-#> 
-#> Chi2 error levels in percent:
-#>          err.min n.optim df
-#> All data   6.398       4 15
-#> parent     6.459       2  7
-#> m1         4.690       2  8
-#> 
-#> Resulting formation fractions:
-#>                 ff
-#> parent_m1   0.5145
-#> parent_sink 0.4855
-#> 
-#> Estimated disappearance times:
-#>           DT50   DT90
-#> parent   7.023  23.33
-#> m1     131.761 437.70
initials <- c("f_parent_to_m1" = 0.5)
+fit.ff.s <- summary(fit.ff)
+print(fit.ff.s$par, 3)
#>                Estimate Std. Error   Lower   Upper
+#> parent_0         99.598     1.6137 96.3257 102.871
+#> log_k_parent     -2.316     0.0419 -2.4006  -2.231
+#> log_k_m1         -5.248     0.1361 -5.5235  -4.972
+#> f_parent_ilr_1    0.041     0.0648 -0.0904   0.172
print(fit.ff.s$bpar, 3)
#>                Estimate se_notrans t value   Pr(>t)    Lower    Upper
+#> parent_0       99.59848   1.613712   61.72 2.02e-38 96.32574 1.03e+02
+#> k_parent        0.09870   0.004132   23.88 5.70e-24  0.09066 1.07e-01
+#> k_m1            0.00526   0.000716    7.35 5.76e-09  0.00399 6.93e-03
+#> f_parent_to_m1  0.51448   0.022880   22.49 4.37e-23  0.46808 5.61e-01
initials <- c("f_parent_to_m1" = 0.5)
 transformed <- transform_odeparms(initials, SFO_SFO.ff)
 backtransform_odeparms(transformed, SFO_SFO.ff)
#> f_parent_to_m1 
 #>            0.5 

@@ -451,70 +259,14 @@ The transformation of sets of formation fractions is fragile, as it supposes
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff.2, data = FALSE)
#> mkin version used for fitting:    0.9.48.1 
-#> R version used for fitting:       3.5.2 
-#> Date of fit:     Mon Mar  4 10:09:31 2019 
-#> Date of summary: Mon Mar  4 10:09:31 2019 
-#> 
-#> Equations:
-#> d_parent/dt = - k_parent * parent
-#> d_m1/dt = + k_parent * parent - k_m1 * m1
-#> 
-#> Model predictions using solution type deSolve 
-#> 
-#> Fitted with method Port using 104 model solutions performed in 0.476 s
-#> 
-#> Weighting: none
-#> 
-#> Starting values for parameters to be optimised:
-#>             value   type
-#> parent_0 100.7500  state
-#> k_parent   0.1000 deparm
-#> k_m1       0.1001 deparm
-#> 
-#> Starting values for the transformed parameters actually optimised:
-#>                   value lower upper
-#> parent_0     100.750000  -Inf   Inf
-#> log_k_parent  -2.302585  -Inf   Inf
-#> log_k_m1      -2.301586  -Inf   Inf
-#> 
-#> Fixed parameter values:
-#>      value  type
-#> m1_0     0 state
-#> 
-#> Optimised, transformed parameters with symmetric confidence intervals:
-#>              Estimate Std. Error Lower  Upper
-#> parent_0       84.790    2.96500 78.78 90.800
-#> log_k_parent   -2.756    0.08088 -2.92 -2.593
-#> log_k_m1       -4.214    0.11150 -4.44 -3.988
-#> 
-#> Parameter correlation:
-#>              parent_0 log_k_parent log_k_m1
-#> parent_0       1.0000      0.11058  0.46156
-#> log_k_parent   0.1106      1.00000  0.06274
-#> log_k_m1       0.4616      0.06274  1.00000
-#> 
-#> Residual standard error: 8.333 on 37 degrees of freedom
-#> 
-#> Backtransformed parameters:
-#> Confidence intervals for internally transformed parameters are asymmetric.
-#> t-test (unrealistically) based on the assumption of normal distribution
-#> for estimators of untransformed parameters.
-#>          Estimate t value    Pr(>t)    Lower    Upper
-#> parent_0 84.79000  28.600 3.939e-27 78.78000 90.80000
-#> k_parent  0.06352  12.360 5.237e-15  0.05392  0.07483
-#> k_m1      0.01478   8.966 4.114e-11  0.01179  0.01853
-#> 
-#> Chi2 error levels in percent:
-#>          err.min n.optim df
-#> All data   19.66       3 16
-#> parent     17.56       2  7
-#> m1         18.71       1  9
-#> 
-#> Estimated disappearance times:
-#>         DT50   DT90
-#> parent 10.91  36.25
-#> m1     46.89 155.75
+fit.ff.2.s <- summary(fit.ff.2) +print(fit.ff.2.s$par, 3)
#> Estimate Std. Error Lower Upper +#> parent_0 84.79 2.9651 78.78 90.80 +#> log_k_parent -2.76 0.0809 -2.92 -2.59 +#> log_k_m1 -4.21 0.1115 -4.44 -3.99
print(fit.ff.2.s$bpar, 3)
#> Estimate se_notrans t value Pr(>t) Lower Upper +#> parent_0 84.7916 2.96505 28.60 3.94e-27 78.7838 90.7994 +#> k_parent 0.0635 0.00514 12.36 5.24e-15 0.0539 0.0748 +#> k_m1 0.0148 0.00165 8.97 4.11e-11 0.0118 0.0185