From 3eefecf0adfbb30b8fb895c244dea6903bcb3e9c Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 31 Jan 2019 16:55:20 +0100 Subject: Restore NAMESPACE which was accidentally overwritten by pkgdown -> roxygen --- docs/reference/mkinfit.html | 906 +++++++++++++++++++++++++++++++++++++++++++- 1 file changed, 890 insertions(+), 16 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index bd691770..42845d68 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -435,40 +435,914 @@

Examples

# Use shorthand notation for parent only degradation
-fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
#> Error in mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(fit)
#> Error in summary(fit): Objekt 'fit' nicht gefunden

+fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
+summary(fit)
#> mkin version used for fitting:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:51:10 2019 
+#> Date of summary: Thu Jan 31 16:51:10 2019 
+#> 
+#> Equations:
+#> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
+#> 
+#> Model predictions using solution type analytical 
+#> 
+#> Fitted with method Port using 64 model solutions performed in 0.162 s
+#> 
+#> Weighting: none
+#> 
+#> Starting values for parameters to be optimised:
+#>          value   type
+#> parent_0  85.1  state
+#> alpha      1.0 deparm
+#> beta      10.0 deparm
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>               value lower upper
+#> parent_0  85.100000  -Inf   Inf
+#> log_alpha  0.000000  -Inf   Inf
+#> log_beta   2.302585  -Inf   Inf
+#> 
+#> Fixed parameter values:
+#> None
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>           Estimate Std. Error    Lower   Upper
+#> parent_0  85.87000     2.2460 80.38000 91.3700
+#> log_alpha  0.05192     0.1605 -0.34080  0.4446
+#> log_beta   0.65100     0.2801 -0.03452  1.3360
+#> 
+#> Parameter correlation:
+#>           parent_0 log_alpha log_beta
+#> parent_0    1.0000   -0.2033  -0.3624
+#> log_alpha  -0.2033    1.0000   0.9547
+#> log_beta   -0.3624    0.9547   1.0000
+#> 
+#> Residual standard error: 2.275 on 6 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   85.870  38.230 1.069e-08 80.3800 91.370
+#> alpha       1.053   6.231 3.953e-04  0.7112  1.560
+#> beta        1.917   3.570 5.895e-03  0.9661  3.806
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.657       3  6
+#> parent     6.657       3  6
+#> 
+#> Estimated disappearance times:
+#>         DT50  DT90 DT50back
+#> parent 1.785 15.15     4.56
+#> 
+#> Data:
+#>  time variable observed predicted residual
+#>     0   parent     85.1    85.875  -0.7749
+#>     1   parent     57.9    55.191   2.7091
+#>     3   parent     29.9    31.845  -1.9452
+#>     7   parent     14.6    17.012  -2.4124
+#>    14   parent      9.7     9.241   0.4590
+#>    28   parent      6.6     4.754   1.8460
+#>    63   parent      4.0     2.102   1.8977
+#>    91   parent      3.9     1.441   2.4590
+#>   119   parent      0.6     1.092  -0.4919

 # One parent compound, one metabolite, both single first order.
 # Use mkinsub for convenience in model formulation. Pathway to sink included per default.
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
#> Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden
# Fit the model to the FOCUS example dataset D using defaults
+  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)))
#> Error in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE): konnte Funktion "mkinfit" nicht finden
#> Timing stopped at: 0 0 0
coef(fit)
#> Error in coef(fit): Objekt 'fit' nicht gefunden
endpoints(fit)
#> Error in endpoints(fit): konnte Funktion "endpoints" nicht finden
# deSolve is slower when no C compiler (gcc) was available during model generation
+                           solution_type = "eigen", quiet = TRUE)))
#>        User      System verstrichen 
+#>       1.022       0.000       1.025 
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 
+#> 
+#> $SFORB
+#> logical(0)
+#> 
+#> $distimes
+#>              DT50      DT90
+#> parent   7.022929  23.32967
+#> m1     131.760712 437.69961
+#> 
# deSolve is slower when no C compiler (gcc) was available during model generation
 print(system.time(fit.deSolve <- mkinfit(SFO_SFO, FOCUS_2006_D,
-                           solution_type = "deSolve")))
#> Error in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve"): konnte Funktion "mkinfit" nicht finden
#> Timing stopped at: 0 0 0
coef(fit.deSolve)
#> Error in coef(fit.deSolve): Objekt 'fit.deSolve' nicht gefunden
endpoints(fit.deSolve)
#> Error in endpoints(fit.deSolve): konnte Funktion "endpoints" nicht finden

+                           solution_type = "deSolve")))
#> Model cost at call  1 :  18915.53 
+#> Model cost at call  2 :  18915.53 
+#> Model cost at call  6 :  11424.02 
+#> Model cost at call  10 :  11424 
+#> Model cost at call  12 :  4094.396 
+#> Model cost at call  16 :  4094.396 
+#> Model cost at call  19 :  1340.595 
+#> Model cost at call  20 :  1340.593 
+#> Model cost at call  25 :  1072.239 
+#> Model cost at call  28 :  1072.236 
+#> Model cost at call  30 :  874.2615 
+#> Model cost at call  33 :  874.2611 
+#> Model cost at call  35 :  616.2377 
+#> Model cost at call  37 :  616.2372 
+#> Model cost at call  40 :  467.4386 
+#> Model cost at call  42 :  467.4381 
+#> Model cost at call  46 :  398.2914 
+#> Model cost at call  48 :  398.2914 
+#> Model cost at call  49 :  398.2913 
+#> Model cost at call  51 :  395.0712 
+#> Model cost at call  54 :  395.0711 
+#> Model cost at call  56 :  378.3298 
+#> Model cost at call  59 :  378.3298 
+#> Model cost at call  62 :  376.9812 
+#> Model cost at call  64 :  376.9811 
+#> Model cost at call  67 :  375.2085 
+#> Model cost at call  69 :  375.2085 
+#> Model cost at call  70 :  375.2085 
+#> Model cost at call  71 :  375.2085 
+#> Model cost at call  72 :  374.5723 
+#> Model cost at call  74 :  374.5723 
+#> Model cost at call  77 :  374.0075 
+#> Model cost at call  79 :  374.0075 
+#> Model cost at call  80 :  374.0075 
+#> Model cost at call  82 :  373.1711 
+#> Model cost at call  84 :  373.1711 
+#> Model cost at call  87 :  372.6445 
+#> Model cost at call  88 :  372.1614 
+#> Model cost at call  90 :  372.1614 
+#> Model cost at call  91 :  372.1614 
+#> Model cost at call  94 :  371.6464 
+#> Model cost at call  99 :  371.4299 
+#> Model cost at call  101 :  371.4299 
+#> Model cost at call  104 :  371.4071 
+#> Model cost at call  106 :  371.4071 
+#> Model cost at call  107 :  371.4071 
+#> Model cost at call  109 :  371.2524 
+#> Model cost at call  113 :  371.2524 
+#> Model cost at call  114 :  371.2136 
+#> Model cost at call  115 :  371.2136 
+#> Model cost at call  116 :  371.2136 
+#> Model cost at call  119 :  371.2134 
+#> Model cost at call  120 :  371.2134 
+#> Model cost at call  122 :  371.2134 
+#> Model cost at call  123 :  371.2134 
+#> Model cost at call  125 :  371.2134 
+#> Model cost at call  126 :  371.2134 
+#> Model cost at call  135 :  371.2134 
+#> Model cost at call  146 :  371.2134 
+#> Optimisation by method Port successfully terminated.
+#>        User      System verstrichen 
+#>       0.823       0.000       0.823 
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 
+#> 
+#> $SFORB
+#> logical(0)
+#> 
+#> $distimes
+#>              DT50      DT90
+#> parent   7.022929  23.32967
+#> m1     131.760711 437.69961
+#> 

 # Use stepwise fitting, using optimised parameters from parent only fit, FOMC
 
FOMC_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub("SFO"))
#> Error in mkinmod(parent = mkinsub("FOMC", "m1"), m1 = mkinsub("SFO")): konnte Funktion "mkinmod" nicht finden
# Fit the model to the FOCUS example dataset D using defaults
-fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
# Use starting parameters from parent only FOMC fit
-fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE,
-  parms.ini = fit.FOMC$bparms.ode)
#> Error in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE, parms.ini = fit.FOMC$bparms.ode): konnte Funktion "mkinfit" nicht finden

+  m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
+fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE)
+# Use starting parameters from parent only FOMC fit
+fit.FOMC = mkinfit("FOMC", FOCUS_2006_D, quiet = TRUE)
+fit.FOMC_SFO <- mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE,
+  parms.ini = fit.FOMC$bparms.ode)
+
 # Use stepwise fitting, using optimised parameters from parent only fit, SFORB
 SFORB_SFO <- mkinmod(
   parent = list(type = "SFORB", to = "m1", sink = TRUE),
-  m1 = list(type = "SFO"))
#> Error in mkinmod(parent = list(type = "SFORB", to = "m1", sink = TRUE),     m1 = list(type = "SFO")): konnte Funktion "mkinmod" nicht finden
# Fit the model to the FOCUS example dataset D using defaults
-fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve",
-                                 quiet = TRUE)
#> Error in mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet = TRUE): konnte Funktion "mkinfit" nicht finden
# Use starting parameters from parent only SFORB fit (not really needed in this case)
-fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)
#> Error in mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode,     quiet = TRUE): konnte Funktion "mkinfit" nicht finden

+  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.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, quiet = TRUE)
+fit.SFORB_SFO.deSolve <- mkinfit(SFORB_SFO, FOCUS_2006_D, solution_type = "deSolve",
+                                 quiet = TRUE)
+# Use starting parameters from parent only SFORB fit (not really needed in this case)
+fit.SFORB = mkinfit("SFORB", FOCUS_2006_D, quiet = TRUE)
+fit.SFORB_SFO <- mkinfit(SFORB_SFO, FOCUS_2006_D, parms.ini = fit.SFORB$bparms.ode, quiet = TRUE)

 
# Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      m1 = mkinsub("SFO"), use_of_ff = "max")
#> Error in mkinmod(parent = mkinsub("SFO", "m1"), m1 = mkinsub("SFO"), use_of_ff = "max"): konnte Funktion "mkinmod" nicht finden
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
#> Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(f.noweight)
#> Error in summary(f.noweight): Objekt 'f.noweight' nicht gefunden
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
#> Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(f.irls)
#> Error in summary(f.irls): Objekt 'f.irls' nicht gefunden
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
#> Error in mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(f.w.mean)
#> Error in summary(f.w.mean): Objekt 'f.w.mean' nicht gefunden
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
-                     quiet = TRUE)
#> Error in mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",     quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(f.w.value)
#> Error in summary(f.w.value): Objekt 'f.w.value' nicht gefunden

+                      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:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:51:22 2019 
+#> Date of summary: Thu Jan 31 16:51:22 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 0.872 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
+#> 
+#> Data:
+#>  time variable observed predicted   residual
+#>     0   parent    99.46  99.59848 -1.385e-01
+#>     0   parent   102.04  99.59848  2.442e+00
+#>     1   parent    93.50  90.23787  3.262e+00
+#>     1   parent    92.50  90.23787  2.262e+00
+#>     3   parent    63.23  74.07319 -1.084e+01
+#>     3   parent    68.99  74.07319 -5.083e+00
+#>     7   parent    52.32  49.91206  2.408e+00
+#>     7   parent    55.13  49.91206  5.218e+00
+#>    14   parent    27.27  25.01257  2.257e+00
+#>    14   parent    26.64  25.01257  1.627e+00
+#>    21   parent    11.50  12.53462 -1.035e+00
+#>    21   parent    11.64  12.53462 -8.946e-01
+#>    35   parent     2.85   3.14787 -2.979e-01
+#>    35   parent     2.91   3.14787 -2.379e-01
+#>    50   parent     0.69   0.71624 -2.624e-02
+#>    50   parent     0.63   0.71624 -8.624e-02
+#>    75   parent     0.05   0.06074 -1.074e-02
+#>    75   parent     0.06   0.06074 -7.381e-04
+#>     0       m1     0.00   0.00000  0.000e+00
+#>     0       m1     0.00   0.00000  0.000e+00
+#>     1       m1     4.84   4.80296  3.704e-02
+#>     1       m1     5.64   4.80296  8.370e-01
+#>     3       m1    12.91  13.02400 -1.140e-01
+#>     3       m1    12.96  13.02400 -6.400e-02
+#>     7       m1    22.97  25.04476 -2.075e+00
+#>     7       m1    24.47  25.04476 -5.748e-01
+#>    14       m1    41.69  36.69002  5.000e+00
+#>    14       m1    33.21  36.69002 -3.480e+00
+#>    21       m1    44.37  41.65310  2.717e+00
+#>    21       m1    46.44  41.65310  4.787e+00
+#>    35       m1    41.22  43.31312 -2.093e+00
+#>    35       m1    37.95  43.31312 -5.363e+00
+#>    50       m1    41.19  41.21831 -2.831e-02
+#>    50       m1    40.01  41.21831 -1.208e+00
+#>    75       m1    40.09  36.44703  3.643e+00
+#>    75       m1    33.85  36.44703 -2.597e+00
+#>   100       m1    31.04  31.98163 -9.416e-01
+#>   100       m1    33.13  31.98163  1.148e+00
+#>   120       m1    25.15  28.78984 -3.640e+00
+#>   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:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:51:24 2019 
+#> Date of summary: Thu Jan 31 16:51:24 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 551 model solutions performed in 2.558 s
+#> 
+#> Weighting: none
+#> 
+#> Iterative reweighting with method obs 
+#> Final mean squared residuals of observed variables:
+#>    parent        m1 
+#> 11.573407  7.407845 
+#> 
+#> 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       99.67000    1.79200 96.04000 103.300
+#> log_k_parent   -2.31200    0.04560 -2.40400  -2.219
+#> log_k_m1       -5.25100    0.12510 -5.50500  -4.998
+#> f_parent_ilr_1  0.03785    0.06318 -0.09027   0.166
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0         1.0000       0.5083  -0.1979        -0.6148
+#> log_k_parent     0.5083       1.0000  -0.3894        -0.6062
+#> log_k_m1        -0.1979      -0.3894   1.0000         0.7417
+#> f_parent_ilr_1  -0.6148      -0.6062   0.7417         1.0000
+#> 
+#> Residual standard error: 1.054 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       99.67000  55.630 8.185e-37 96.040000 1.033e+02
+#> k_parent        0.09906  21.930 1.016e-22  0.090310 1.087e-01
+#> k_m1            0.00524   7.996 8.486e-10  0.004066 6.753e-03
+#> f_parent_to_m1  0.51340  23.000 2.038e-23  0.468100 5.584e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.399       4 15
+#> parent     6.466       2  7
+#> m1         4.679       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5134
+#> parent_sink 0.4866
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   6.997  23.24
+#> m1     132.282 439.43
+#> 
+#> Data:
+#>  time variable observed predicted   residual   err
+#>     0   parent    99.46  99.67218 -2.122e-01 3.402
+#>     0   parent   102.04  99.67218  2.368e+00 3.402
+#>     1   parent    93.50  90.27153  3.228e+00 3.402
+#>     1   parent    92.50  90.27153  2.228e+00 3.402
+#>     3   parent    63.23  74.04648 -1.082e+01 3.402
+#>     3   parent    68.99  74.04648 -5.056e+00 3.402
+#>     7   parent    52.32  49.82092  2.499e+00 3.402
+#>     7   parent    55.13  49.82092  5.309e+00 3.402
+#>    14   parent    27.27  24.90288  2.367e+00 3.402
+#>    14   parent    26.64  24.90288  1.737e+00 3.402
+#>    21   parent    11.50  12.44765 -9.476e-01 3.402
+#>    21   parent    11.64  12.44765 -8.076e-01 3.402
+#>    35   parent     2.85   3.11002 -2.600e-01 3.402
+#>    35   parent     2.91   3.11002 -2.000e-01 3.402
+#>    50   parent     0.69   0.70374 -1.374e-02 3.402
+#>    50   parent     0.63   0.70374 -7.374e-02 3.402
+#>    75   parent     0.05   0.05913 -9.134e-03 3.402
+#>    75   parent     0.06   0.05913  8.662e-04 3.402
+#>     0       m1     0.00   0.00000  0.000e+00 2.722
+#>     0       m1     0.00   0.00000  0.000e+00 2.722
+#>     1       m1     4.84   4.81328  2.672e-02 2.722
+#>     1       m1     5.64   4.81328  8.267e-01 2.722
+#>     3       m1    12.91  13.04779 -1.378e-01 2.722
+#>     3       m1    12.96  13.04779 -8.779e-02 2.722
+#>     7       m1    22.97  25.07615 -2.106e+00 2.722
+#>     7       m1    24.47  25.07615 -6.062e-01 2.722
+#>    14       m1    41.69  36.70729  4.983e+00 2.722
+#>    14       m1    33.21  36.70729 -3.497e+00 2.722
+#>    21       m1    44.37  41.65050  2.720e+00 2.722
+#>    21       m1    46.44  41.65050  4.790e+00 2.722
+#>    35       m1    41.22  43.28866 -2.069e+00 2.722
+#>    35       m1    37.95  43.28866 -5.339e+00 2.722
+#>    50       m1    41.19  41.19339 -3.386e-03 2.722
+#>    50       m1    40.01  41.19339 -1.183e+00 2.722
+#>    75       m1    40.09  36.43820  3.652e+00 2.722
+#>    75       m1    33.85  36.43820 -2.588e+00 2.722
+#>   100       m1    31.04  31.98971 -9.497e-01 2.722
+#>   100       m1    33.13  31.98971  1.140e+00 2.722
+#>   120       m1    25.15  28.80898 -3.659e+00 2.722
+#>   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:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:51:25 2019 
+#> Date of summary: Thu Jan 31 16:51:25 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 155 model solutions performed in 0.711 s
+#> 
+#> Weighting: mean
+#> 
+#> 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        99.7300    1.93200 95.81000 103.6000
+#> log_k_parent    -2.3090    0.04837 -2.40700  -2.2110
+#> log_k_m1        -5.2550    0.12070 -5.49900  -5.0100
+#> f_parent_ilr_1   0.0354    0.06344 -0.09327   0.1641
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0         1.0000       0.5004  -0.2143        -0.6514
+#> log_k_parent     0.5004       1.0000  -0.4282        -0.6383
+#> log_k_m1        -0.2143      -0.4282   1.0000         0.7390
+#> f_parent_ilr_1  -0.6514      -0.6383   0.7390         1.0000
+#> 
+#> Residual standard error: 0.09829 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       99.730000  51.630 1.166e-35 95.81000 1.036e+02
+#> k_parent        0.099360  20.670 7.304e-22  0.09007 1.096e-01
+#> k_m1            0.005224   8.287 3.649e-10  0.00409 6.672e-03
+#> f_parent_to_m1  0.512500  22.860 2.497e-23  0.46710 5.578e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.401       4 15
+#> parent     6.473       2  7
+#> m1         4.671       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5125
+#> parent_sink 0.4875
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   6.976  23.18
+#> m1     132.696 440.81
+#> 
+#> Data:
+#>  time variable observed predicted   residual
+#>     0   parent    99.46  99.73057  -0.270570
+#>     0   parent   102.04  99.73057   2.309430
+#>     1   parent    93.50  90.29805   3.201945
+#>     1   parent    92.50  90.29805   2.201945
+#>     3   parent    63.23  74.02503 -10.795028
+#>     3   parent    68.99  74.02503  -5.035028
+#>     7   parent    52.32  49.74838   2.571618
+#>     7   parent    55.13  49.74838   5.381618
+#>    14   parent    27.27  24.81588   2.454124
+#>    14   parent    26.64  24.81588   1.824124
+#>    21   parent    11.50  12.37885  -0.878849
+#>    21   parent    11.64  12.37885  -0.738849
+#>    35   parent     2.85   3.08022  -0.230219
+#>    35   parent     2.91   3.08022  -0.170219
+#>    50   parent     0.69   0.69396  -0.003958
+#>    50   parent     0.63   0.69396  -0.063958
+#>    75   parent     0.05   0.05789  -0.007888
+#>    75   parent     0.06   0.05789   0.002112
+#>     0       m1     0.00   0.00000   0.000000
+#>     0       m1     0.00   0.00000   0.000000
+#>     1       m1     4.84   4.82149   0.018512
+#>     1       m1     5.64   4.82149   0.818512
+#>     3       m1    12.91  13.06669  -0.156692
+#>     3       m1    12.96  13.06669  -0.106692
+#>     7       m1    22.97  25.10106  -2.131058
+#>     7       m1    24.47  25.10106  -0.631058
+#>    14       m1    41.69  36.72092   4.969077
+#>    14       m1    33.21  36.72092  -3.510923
+#>    21       m1    44.37  41.64835   2.721647
+#>    21       m1    46.44  41.64835   4.791647
+#>    35       m1    41.22  43.26923  -2.049225
+#>    35       m1    37.95  43.26923  -5.319225
+#>    50       m1    41.19  41.17364   0.016361
+#>    50       m1    40.01  41.17364  -1.163639
+#>    75       m1    40.09  36.43122   3.658776
+#>    75       m1    33.85  36.43122  -2.581224
+#>   100       m1    31.04  31.99612  -0.956124
+#>   100       m1    33.13  31.99612   1.133876
+#>   120       m1    25.15  28.82413  -3.674128
+#>   120       m1    33.31  28.82413   4.485872
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
+                     quiet = TRUE)
+summary(f.w.value)
#> mkin version used for fitting:    0.9.47.6 
+#> R version used for fitting:       3.5.2 
+#> Date of fit:     Thu Jan 31 16:51:26 2019 
+#> Date of summary: Thu Jan 31 16:51:26 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 174 model solutions performed in 0.807 s
+#> 
+#> Weighting: manual
+#> 
+#> 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        99.6600   2.712000 94.14000 105.2000
+#> log_k_parent    -2.2980   0.008118 -2.31500  -2.2820
+#> log_k_m1        -5.2410   0.096690 -5.43800  -5.0450
+#> f_parent_ilr_1   0.0231   0.057990 -0.09474   0.1409
+#> 
+#> Parameter correlation:
+#>                parent_0 log_k_parent log_k_m1 f_parent_ilr_1
+#> parent_0        1.00000       0.6843 -0.08687        -0.7564
+#> log_k_parent    0.68435       1.0000 -0.12695        -0.5812
+#> log_k_m1       -0.08687      -0.1269  1.00000         0.5195
+#> f_parent_ilr_1 -0.75644      -0.5812  0.51952         1.0000
+#> 
+#> Residual standard error: 0.08396 on 34 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       99.660000   36.75 2.957e-29 94.14000 1.052e+02
+#> k_parent        0.100400  123.20 5.927e-47  0.09878 1.021e-01
+#> k_m1            0.005295   10.34 2.447e-12  0.00435 6.444e-03
+#> f_parent_to_m1  0.508200   24.79 1.184e-23  0.46660 5.497e-01
+#> 
+#> Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   6.461       4 15
+#> parent     6.520       2  7
+#> m1         4.744       2  8
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_m1   0.5082
+#> parent_sink 0.4918
+#> 
+#> Estimated disappearance times:
+#>           DT50   DT90
+#> parent   6.902  22.93
+#> m1     130.916 434.89
+#> 
+#> Data:
+#>  time variable observed predicted   residual    err
+#>     0   parent    99.46  99.65571  -0.195715  99.46
+#>     0   parent   102.04  99.65571   2.384285 102.04
+#>     1   parent    93.50  90.13383   3.366170  93.50
+#>     1   parent    92.50  90.13383   2.366170  92.50
+#>     3   parent    63.23  73.73252 -10.502518  63.23
+#>     3   parent    68.99  73.73252  -4.742518  68.99
+#>     7   parent    52.32  49.34027   2.979728  52.32
+#>     7   parent    55.13  49.34027   5.789728  55.13
+#>    14   parent    27.27  24.42873   2.841271  27.27
+#>    14   parent    26.64  24.42873   2.211271  26.64
+#>    21   parent    11.50  12.09484  -0.594842  11.50
+#>    21   parent    11.64  12.09484  -0.454842  11.64
+#>    35   parent     2.85   2.96482  -0.114824   2.85
+#>    35   parent     2.91   2.96482  -0.054824   2.91
+#>    50   parent     0.69   0.65733   0.032670   0.69
+#>    50   parent     0.63   0.65733  -0.027330   0.63
+#>    75   parent     0.05   0.05339  -0.003386   0.05
+#>    75   parent     0.06   0.05339   0.006614   0.06
+#>     1       m1     4.84   4.82570   0.014301   4.84
+#>     1       m1     5.64   4.82570   0.814301   5.64
+#>     3       m1    12.91  13.06402  -0.154020  12.91
+#>     3       m1    12.96  13.06402  -0.104020  12.96
+#>     7       m1    22.97  25.04656  -2.076564  22.97
+#>     7       m1    24.47  25.04656  -0.576564  24.47
+#>    14       m1    41.69  36.53601   5.153988  41.69
+#>    14       m1    33.21  36.53601  -3.326012  33.21
+#>    21       m1    44.37  41.34639   3.023609  44.37
+#>    21       m1    46.44  41.34639   5.093609  46.44
+#>    35       m1    41.22  42.82669  -1.606690  41.22
+#>    35       m1    37.95  42.82669  -4.876690  37.95
+#>    50       m1    41.19  40.67342   0.516578  41.19
+#>    50       m1    40.01  40.67342  -0.663422  40.01
+#>    75       m1    40.09  35.91105   4.178947  40.09
+#>    75       m1    33.85  35.91105  -2.061053  33.85
+#>   100       m1    31.04  31.48161  -0.441612  31.04
+#>   100       m1    33.13  31.48161   1.648388  33.13
+#>   120       m1    25.15  28.32018  -3.170181  25.15
+#>   120       m1    33.31  28.32018   4.989819  33.31

 
# Manual weighting
 dw <- FOCUS_2006_D
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
-f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
#> Error in mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE): konnte Funktion "mkinfit" nicht finden
summary(f.w.man)
#> Error in summary(f.w.man): Objekt 'f.w.man' nicht gefunden
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
-                       reweight.method = "obs")
#> Error in mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE, reweight.method = "obs"): konnte Funktion "mkinfit" nicht finden
summary(f.w.man.irls)
#> Error in summary(f.w.man.irls): Objekt 'f.w.man.irls' nicht gefunden
+f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE) +summary(f.w.man)
#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:28 2019 +#> Date of summary: Thu Jan 31 16:51:28 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 270 model solutions performed in 1.257 s +#> +#> Weighting: manual +#> +#> 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 99.49000 1.33200 96.7800 102.2000 +#> log_k_parent -2.32100 0.03550 -2.3930 -2.2490 +#> log_k_m1 -5.24100 0.21280 -5.6730 -4.8100 +#> f_parent_ilr_1 0.04571 0.08966 -0.1361 0.2275 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.00000 0.5312 -0.09456 -0.3351 +#> log_k_parent 0.53123 1.0000 -0.17800 -0.3360 +#> log_k_m1 -0.09456 -0.1780 1.00000 0.7616 +#> f_parent_ilr_1 -0.33514 -0.3360 0.76156 1.0000 +#> +#> Residual standard error: 2.628 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 99.490000 74.69 2.221e-41 96.780000 1.022e+02 +#> k_parent 0.098140 28.17 2.012e-26 0.091320 1.055e-01 +#> k_m1 0.005292 4.70 1.873e-05 0.003437 8.148e-03 +#> f_parent_to_m1 0.516200 16.30 1.686e-18 0.452000 5.798e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.400 4 15 +#> parent 6.454 2 7 +#> m1 4.708 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5162 +#> parent_sink 0.4838 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 7.063 23.46 +#> m1 130.971 435.08 +#> +#> Data: +#> time variable observed predicted residual err +#> 0 parent 99.46 99.48598 -0.025979 1 +#> 0 parent 102.04 99.48598 2.554021 1 +#> 1 parent 93.50 90.18612 3.313880 1 +#> 1 parent 92.50 90.18612 2.313880 1 +#> 3 parent 63.23 74.11316 -10.883163 1 +#> 3 parent 68.99 74.11316 -5.123163 1 +#> 7 parent 52.32 50.05030 2.269705 1 +#> 7 parent 55.13 50.05030 5.079705 1 +#> 14 parent 27.27 25.17975 2.090250 1 +#> 14 parent 26.64 25.17975 1.460250 1 +#> 21 parent 11.50 12.66765 -1.167654 1 +#> 21 parent 11.64 12.66765 -1.027654 1 +#> 35 parent 2.85 3.20616 -0.356164 1 +#> 35 parent 2.91 3.20616 -0.296164 1 +#> 50 parent 0.69 0.73562 -0.045619 1 +#> 50 parent 0.63 0.73562 -0.105619 1 +#> 75 parent 0.05 0.06326 -0.013256 1 +#> 75 parent 0.06 0.06326 -0.003256 1 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 0 m1 0.00 0.00000 0.000000 2 +#> 1 m1 4.84 4.78729 0.052713 2 +#> 1 m1 5.64 4.78729 0.852713 2 +#> 3 m1 12.91 12.98785 -0.077848 2 +#> 3 m1 12.96 12.98785 -0.027848 2 +#> 7 m1 22.97 24.99695 -2.026946 2 +#> 7 m1 24.47 24.99695 -0.526946 2 +#> 14 m1 41.69 36.66353 5.026472 2 +#> 14 m1 33.21 36.66353 -3.453528 2 +#> 21 m1 44.37 41.65681 2.713186 2 +#> 21 m1 46.44 41.65681 4.783186 2 +#> 35 m1 41.22 43.35031 -2.130314 2 +#> 35 m1 37.95 43.35031 -5.400314 2 +#> 50 m1 41.19 41.25637 -0.066368 2 +#> 50 m1 40.01 41.25637 -1.246368 2 +#> 75 m1 40.09 36.46057 3.629429 2 +#> 75 m1 33.85 36.46057 -2.610571 2 +#> 100 m1 31.04 31.96929 -0.929293 2 +#> 100 m1 33.13 31.96929 1.160707 2 +#> 120 m1 25.15 28.76062 -3.610621 2 +#> 120 m1 33.31 28.76062 4.549379 2
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE, + reweight.method = "obs") +summary(f.w.man.irls)
#> mkin version used for fitting: 0.9.47.6 +#> R version used for fitting: 3.5.2 +#> Date of fit: Thu Jan 31 16:51:31 2019 +#> Date of summary: Thu Jan 31 16:51:31 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 692 model solutions performed in 3.3 s +#> +#> Weighting: manual +#> +#> Iterative reweighting with method obs +#> Final mean squared residuals of observed variables: +#> parent m1 +#> 11.573406 7.407846 +#> +#> 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 99.67000 1.79200 96.04000 103.300 +#> log_k_parent -2.31200 0.04560 -2.40400 -2.220 +#> log_k_m1 -5.25100 0.12510 -5.50500 -4.998 +#> f_parent_ilr_1 0.03785 0.06318 -0.09027 0.166 +#> +#> Parameter correlation: +#> parent_0 log_k_parent log_k_m1 f_parent_ilr_1 +#> parent_0 1.0000 0.5083 -0.1979 -0.6148 +#> log_k_parent 0.5083 1.0000 -0.3894 -0.6062 +#> log_k_m1 -0.1979 -0.3894 1.0000 0.7417 +#> f_parent_ilr_1 -0.6148 -0.6062 0.7417 1.0000 +#> +#> Residual standard error: 1.054 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 99.67000 55.630 8.185e-37 96.040000 1.033e+02 +#> k_parent 0.09906 21.930 1.016e-22 0.090310 1.087e-01 +#> k_m1 0.00524 7.996 8.486e-10 0.004066 6.753e-03 +#> f_parent_to_m1 0.51340 23.000 2.039e-23 0.468100 5.584e-01 +#> +#> Chi2 error levels in percent: +#> err.min n.optim df +#> All data 6.399 4 15 +#> parent 6.466 2 7 +#> m1 4.679 2 8 +#> +#> Resulting formation fractions: +#> ff +#> parent_m1 0.5134 +#> parent_sink 0.4866 +#> +#> Estimated disappearance times: +#> DT50 DT90 +#> parent 6.997 23.24 +#> m1 132.282 439.43 +#> +#> Data: +#> time variable observed predicted residual err.ini err +#> 0 parent 99.46 99.67217 -2.122e-01 1 3.402 +#> 0 parent 102.04 99.67217 2.368e+00 1 3.402 +#> 1 parent 93.50 90.27152 3.228e+00 1 3.402 +#> 1 parent 92.50 90.27152 2.228e+00 1 3.402 +#> 3 parent 63.23 74.04648 -1.082e+01 1 3.402 +#> 3 parent 68.99 74.04648 -5.056e+00 1 3.402 +#> 7 parent 52.32 49.82092 2.499e+00 1 3.402 +#> 7 parent 55.13 49.82092 5.309e+00 1 3.402 +#> 14 parent 27.27 24.90288 2.367e+00 1 3.402 +#> 14 parent 26.64 24.90288 1.737e+00 1 3.402 +#> 21 parent 11.50 12.44765 -9.477e-01 1 3.402 +#> 21 parent 11.64 12.44765 -8.077e-01 1 3.402 +#> 35 parent 2.85 3.11002 -2.600e-01 1 3.402 +#> 35 parent 2.91 3.11002 -2.000e-01 1 3.402 +#> 50 parent 0.69 0.70375 -1.375e-02 1 3.402 +#> 50 parent 0.63 0.70375 -7.375e-02 1 3.402 +#> 75 parent 0.05 0.05913 -9.134e-03 1 3.402 +#> 75 parent 0.06 0.05913 8.661e-04 1 3.402 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 0 m1 0.00 0.00000 0.000e+00 2 2.722 +#> 1 m1 4.84 4.81328 2.672e-02 2 2.722 +#> 1 m1 5.64 4.81328 8.267e-01 2 2.722 +#> 3 m1 12.91 13.04779 -1.378e-01 2 2.722 +#> 3 m1 12.96 13.04779 -8.779e-02 2 2.722 +#> 7 m1 22.97 25.07615 -2.106e+00 2 2.722 +#> 7 m1 24.47 25.07615 -6.062e-01 2 2.722 +#> 14 m1 41.69 36.70729 4.983e+00 2 2.722 +#> 14 m1 33.21 36.70729 -3.497e+00 2 2.722 +#> 21 m1 44.37 41.65050 2.719e+00 2 2.722 +#> 21 m1 46.44 41.65050 4.789e+00 2 2.722 +#> 35 m1 41.22 43.28866 -2.069e+00 2 2.722 +#> 35 m1 37.95 43.28866 -5.339e+00 2 2.722 +#> 50 m1 41.19 41.19339 -3.387e-03 2 2.722 +#> 50 m1 40.01 41.19339 -1.183e+00 2 2.722 +#> 75 m1 40.09 36.43820 3.652e+00 2 2.722 +#> 75 m1 33.85 36.43820 -2.588e+00 2 2.722 +#> 100 m1 31.04 31.98971 -9.497e-01 2 2.722 +#> 100 m1 33.13 31.98971 1.140e+00 2 2.722 +#> 120 m1 25.15 28.80897 -3.659e+00 2 2.722 +#> 120 m1 33.31 28.80897 4.501e+00 2 2.722