From 575fcacaa33076de97f41a79afb37efb97ca82e0 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Mon, 30 Mar 2020 21:43:10 +0200 Subject: Static documentation rebuilt by pkgdown --- docs/reference/mkinfit.html | 109 +++++++++++++++++++++++++------------------- 1 file changed, 62 insertions(+), 47 deletions(-) (limited to 'docs/reference/mkinfit.html') diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 7ee73f15..ffc8d52b 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -75,7 +75,7 @@ likelihood function." /> mkin - 0.9.49.6 + 0.9.49.9 @@ -148,18 +148,33 @@ degradation model parameters, as both of them are arguments of the likelihood function.

- 
mkinfit(mkinmod, observed, parms.ini = "auto", state.ini = "auto",
-  err.ini = "auto", fixed_parms = NULL,
-  fixed_initials = names(mkinmod$diffs)[-1], from_max_mean = FALSE,
+    
mkinfit(
+  mkinmod,
+  observed,
+  parms.ini = "auto",
+  state.ini = "auto",
+  err.ini = "auto",
+  fixed_parms = NULL,
+  fixed_initials = names(mkinmod$diffs)[-1],
+  from_max_mean = FALSE,
   solution_type = c("auto", "analytical", "eigen", "deSolve"),
-  method.ode = "lsoda", use_compiled = "auto",
+  method.ode = "lsoda",
+  use_compiled = "auto",
   control = list(eval.max = 300, iter.max = 200),
-  transform_rates = TRUE, transform_fractions = TRUE, quiet = FALSE,
-  atol = 1e-08, rtol = 1e-10, n.outtimes = 100,
+  transform_rates = TRUE,
+  transform_fractions = TRUE,
+  quiet = FALSE,
+  atol = 1e-08,
+  rtol = 1e-10,
+  n.outtimes = 100,
   error_model = c("const", "obs", "tc"),
-  error_model_algorithm = c("auto", "d_3", "direct", "twostep",
-  "threestep", "fourstep", "IRLS", "OLS"), reweight.tol = 1e-08,
-  reweight.max.iter = 10, trace_parms = FALSE, ...)

+  error_model_algorithm = c("auto", "d_3", "direct", "twostep", "threestep", "fourstep",
+    "IRLS", "OLS"),
+  reweight.tol = 1e-08,
+  reweight.max.iter = 10,
+  trace_parms = FALSE,
+  ...
+)

Arguments

@@ -400,17 +415,17 @@ estimators.


 # Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:21 2019 
-#> Date of summary: Fri Nov  1 10:08:21 2019 
+summary(fit)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:20 2020 
+#> Date of summary: Mon Mar 30 21:41:20 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted using 222 model solutions performed in 0.456 s
+#> Fitted using 222 model solutions performed in 0.463 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -440,10 +455,10 @@ estimators.

 #> 
 #> Parameter correlation:
 #>             parent_0  log_alpha   log_beta     sigma
-#> parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.770e-08
-#> log_alpha -1.565e-01  1.000e+00  9.564e-01 9.974e-08
-#> log_beta  -3.142e-01  9.564e-01  1.000e+00 8.468e-08
-#> sigma      4.770e-08  9.974e-08  8.468e-08 1.000e+00
+#> parent_0   1.000e+00 -1.565e-01 -3.142e-01 4.758e-08
+#> log_alpha -1.565e-01  1.000e+00  9.564e-01 1.007e-07
+#> log_beta  -3.142e-01  9.564e-01  1.000e+00 8.568e-08
+#> sigma      4.758e-08  1.007e-07  8.568e-08 1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -482,7 +497,7 @@ estimators.

   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)))
#> Warning: Observations with value of zero were removed from the data
#>        User      System verstrichen 
-#>       1.488       0.000       1.491 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
+#>       1.526       0.000       1.530 
coef(fit)
#> NULL
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -533,9 +548,9 @@ estimators.

 #> Sum of squared residuals at call 82: 373.1711
 #> Sum of squared residuals at call 84: 373.1711
 #> Sum of squared residuals at call 87: 372.6445
-#> Sum of squared residuals at call 88: 372.1615
-#> Sum of squared residuals at call 90: 372.1615
-#> Sum of squared residuals at call 91: 372.1615
+#> Sum of squared residuals at call 88: 372.1614
+#> Sum of squared residuals at call 90: 372.1614
+#> Sum of squared residuals at call 91: 372.1614
 #> Sum of squared residuals at call 94: 371.6464
 #> Sum of squared residuals at call 99: 371.4299
 #> Sum of squared residuals at call 101: 371.4299
@@ -555,7 +570,7 @@ estimators.

 #> Sum of squared residuals at call 126: 371.2134
 #> Sum of squared residuals at call 135: 371.2134
 #> Negative log-likelihood at call 145: 97.22429
#> Optimisation successfully terminated.
#>        User      System verstrichen 
-#>       1.058       0.000       1.059 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
+#>       1.083       0.000       1.084 
coef(fit.deSolve)
#> NULL
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
 #> 
@@ -589,10 +604,10 @@ estimators.

 # \dontrun{
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
-                      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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:36 2019 
-#> Date of summary: Fri Nov  1 10:08:36 2019 
+                      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)
#> Warning: Observations with value of zero were removed from the data
summary(f.noweight)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:36 2020 
+#> Date of summary: Mon Mar 30 21:41:36 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -600,7 +615,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 421 model solutions performed in 1.083 s
+#> Fitted using 422 model solutions performed in 1.144 s
 #> 
 #> Error model: Constant variance 
 #> 
@@ -634,11 +649,11 @@ estimators.

 #> 
 #> Parameter correlation:
 #>                  parent_0 log_k_parent   log_k_m1 f_parent_ilr_1      sigma
-#> parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -2.265e-07
-#> log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.785e-07
-#> log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.386e-07
-#> f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -3.641e-08
-#> sigma          -2.265e-07    3.785e-07 -1.386e-07     -3.641e-08  1.000e+00
+#> parent_0        1.000e+00    5.174e-01 -1.688e-01     -5.471e-01 -2.443e-07
+#> log_k_parent    5.174e-01    1.000e+00 -3.263e-01     -5.426e-01  3.181e-07
+#> log_k_m1       -1.688e-01   -3.263e-01  1.000e+00      7.478e-01 -1.369e-07
+#> f_parent_ilr_1 -5.471e-01   -5.426e-01  7.478e-01      1.000e+00 -2.287e-08
+#> sigma          -2.443e-07    3.181e-07 -1.369e-07     -2.287e-08  1.000e+00
 #> 
 #> Backtransformed parameters:
 #> Confidence intervals for internally transformed parameters are asymmetric.
@@ -706,10 +721,10 @@ estimators.

 #>   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.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:39 2019 
-#> Date of summary: Fri Nov  1 10:08:39 2019 
+#>   120       m1    33.31  28.78984  4.520e+00
f.obs <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "obs", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.obs)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:39 2020 
+#> Date of summary: Mon Mar 30 21:41:39 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -717,7 +732,7 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 978 model solutions performed in 2.553 s
+#> Fitted using 979 model solutions performed in 2.576 s
 #> 
 #> Error model: Variance unique to each observed variable 
 #> 
@@ -838,10 +853,10 @@ estimators.

 #>   100       m1    31.04  31.98773 -9.477e-01
 #>   100       m1    33.13  31.98773  1.142e+00
 #>   120       m1    25.15  28.80429 -3.654e+00
-#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.6 
-#> R version used for fitting:       3.6.1 
-#> Date of fit:     Fri Nov  1 10:08:48 2019 
-#> Date of summary: Fri Nov  1 10:08:48 2019 
+#>   120       m1    33.31  28.80429  4.506e+00
f.tc <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, error_model = "tc", quiet = TRUE)
#> Warning: Observations with value of zero were removed from the data
summary(f.tc)
#> mkin version used for fitting:    0.9.49.9 
+#> R version used for fitting:       3.6.3 
+#> Date of fit:     Mon Mar 30 21:41:50 2020 
+#> Date of summary: Mon Mar 30 21:41:50 2020 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -849,12 +864,12 @@ estimators.

 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted using 2289 model solutions performed in 9.253 s
+#> Fitted using 2552 model solutions performed in 10.593 s
 #> 
 #> Error model: Two-component variance function 
 #> 
 #> Error model algorithm: d_3 
-#> Direct fitting and three-step fitting yield approximately the same likelihood 
+#> Three-step fitting yielded a higher likelihood than direct fitting 
 #> 
 #> Starting values for parameters to be optimised:
 #>                   value   type
@@ -960,8 +975,8 @@ estimators.

 #>    50       m1    40.01  41.34199  -1.331985
 #>    75       m1    40.09  36.61471   3.475295
 #>    75       m1    33.85  36.61471  -2.764705
-#>   100       m1    31.04  32.20082  -1.160823
-#>   100       m1    33.13  32.20082   0.929177
+#>   100       m1    31.04  32.20082  -1.160824
+#>   100       m1    33.13  32.20082   0.929176
 #>   120       m1    25.15  29.04130  -3.891304
 #>   120       m1    33.31  29.04130   4.268696
# }
 
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