From a7beb73cdfeed34525266d76f424375e1d069a48 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 19 Sep 2019 12:43:04 +0200 Subject: Static documentation rebuilt by pkgdown Use lazy = TRUE in the pd target for generating pkgdown documentation --- docs/reference/synthetic_data_for_UBA_2014.html | 462 ++++++++++++++++++++++++ 1 file changed, 462 insertions(+) create mode 100644 docs/reference/synthetic_data_for_UBA_2014.html (limited to 'docs/reference/synthetic_data_for_UBA_2014.html') diff --git a/docs/reference/synthetic_data_for_UBA_2014.html b/docs/reference/synthetic_data_for_UBA_2014.html new file mode 100644 index 00000000..2c4480d9 --- /dev/null +++ b/docs/reference/synthetic_data_for_UBA_2014.html @@ -0,0 +1,462 @@ + + + + + + + + +Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+

Synthetic datasets for one parent compound with two metabolites

+ + +
+ +
+ +

The 12 datasets were generated using four different models and three different + variance components. The four models are either the SFO or the DFOP model with either + two sequential or two parallel metabolites.

+

Variance component 'a' is based on a normal distribution with standard deviation of 3, + Variance component 'b' is also based on a normal distribution, but with a standard deviation of 7. + Variance component 'c' is based on the error model from Rocke and Lorenzato (1995), with the + minimum standard deviation (for small y values) of 0.5, and a proportionality constant of 0.07 + for the increase of the standard deviation with y. Note that this is a simplified version + of the error model proposed by Rocke and Lorenzato (1995), as in their model the error of the + measured values approximates lognormal distribution for high values, whereas we are using + normally distributed error components all along.

+

Initial concentrations for metabolites and all values where adding the variance component resulted + in a value below the assumed limit of detection of 0.1 were set to NA.

+

As an example, the first dataset has the title SFO_lin_a and is based on the SFO model + with two sequential metabolites (linear pathway), with added variance component 'a'.

+

Compare also the code in the example section to see the degradation models.

+ +
+ + 
synthetic_data_for_UBA_2014
+ +

Format

+ +

A list containing twelve datasets as an R6 class defined by mkinds, + each containing, among others, the following components

+
title

The name of the dataset, e.g. SFO_lin_a

+
data

A data frame with the data in the form expected by mkinfit

+ +
+ + +

Source

+ +

Ranke (2014) Prüfung und Validierung von Modellierungssoftware als Alternative + zu ModelMaker 4.0, Umweltbundesamt Projektnummer 27452

+

Rocke, David M. und Lorenzato, Stefan (1995) A two-component model for + measurement error in analytical chemistry. Technometrics 37(2), 176-184.

+ + +

Examples

+ 
# The data have been generated using the following kinetic models
+m_synth_SFO_lin <- mkinmod(parent = list(type = "SFO", to = "M1"),
+                           M1 = list(type = "SFO", to = "M2"),
+                           M2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

+
+m_synth_SFO_par <- mkinmod(parent = list(type = "SFO", to = c("M1", "M2"),
+                                         sink = FALSE),
+                           M1 = list(type = "SFO"),
+                           M2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

+m_synth_DFOP_lin <- mkinmod(parent = list(type = "DFOP", to = "M1"),
+                            M1 = list(type = "SFO", to = "M2"),
+                            M2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

+m_synth_DFOP_par <- mkinmod(parent = list(type = "DFOP", to = c("M1", "M2"),
+                                          sink = FALSE),
+                            M1 = list(type = "SFO"),
+                            M2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

+# The model predictions without intentional error were generated as follows
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+
+d_synth_SFO_lin <- mkinpredict(m_synth_SFO_lin,
+                               c(k_parent = 0.7, f_parent_to_M1 = 0.8,
+                                 k_M1 = 0.3, f_M1_to_M2 = 0.7,
+                                 k_M2 = 0.02),
+                               c(parent = 100, M1 = 0, M2 = 0),
+                               sampling_times)
+
+d_synth_DFOP_lin <- mkinpredict(m_synth_DFOP_lin,
+                                c(k1 = 0.2, k2 = 0.02, g = 0.5,
+                                  f_parent_to_M1 = 0.5, k_M1 = 0.3,
+                                  f_M1_to_M2 = 0.7, k_M2 = 0.02),
+                                 c(parent = 100, M1 = 0, M2 = 0),
+                                 sampling_times)
+
+d_synth_SFO_par <- mkinpredict(m_synth_SFO_par,
+                               c(k_parent = 0.2,
+                                 f_parent_to_M1 = 0.8, k_M1 = 0.01,
+                                 f_parent_to_M2 = 0.2, k_M2 = 0.02),
+                                 c(parent = 100, M1 = 0, M2 = 0),
+                                 sampling_times)
+
+d_synth_DFOP_par <- mkinpredict(m_synth_DFOP_par,
+                               c(k1 = 0.3, k2 = 0.02, g = 0.7,
+                                 f_parent_to_M1 = 0.6, k_M1 = 0.04,
+                                 f_parent_to_M2 = 0.4, k_M2 = 0.01),
+                                 c(parent = 100, M1 = 0, M2 = 0),
+                                 sampling_times)
+
+# Construct names for datasets with errors
+d_synth_names = paste0("d_synth_", c("SFO_lin", "SFO_par",
+                                     "DFOP_lin", "DFOP_par"))
+
+# Original function used or adding errors. The add_err function now published
+# with this package is a slightly generalised version where the names of
+# secondary compartments that should have an initial value of zero (M1 and M2
+# in this case) are not hardcoded any more.
+# add_err = function(d, sdfunc, LOD = 0.1, reps = 2, seed = 123456789)
+# {
+#   set.seed(seed)
+#   d_long = mkin_wide_to_long(d, time = "time")
+#   d_rep = data.frame(lapply(d_long, rep, each = 2))
+#   d_rep$value = rnorm(length(d_rep$value), d_rep$value, sdfunc(d_rep$value))
+#
+#   d_rep[d_rep$time == 0 & match(d_rep$name, c("M1", "M2"), "value"] <- 0
+#   d_NA <- transform(d_rep, value = ifelse(value < LOD, NA, value))
+#   d_NA$value <- round(d_NA$value, 1)
+#   return(d_NA)
+# }
+
+# The following is the simplified version of the two-component model of Rocke
+# and Lorenzato (1995)
+sdfunc_twocomp = function(value, sd_low, rsd_high) {
+  sqrt(sd_low^2 + value^2 * rsd_high^2)
+}
+
+# Add the errors.
+for (d_synth_name in d_synth_names)
+{
+  d_synth = get(d_synth_name)
+  assign(paste0(d_synth_name, "_a"), add_err(d_synth, function(value) 3))
+  assign(paste0(d_synth_name, "_b"), add_err(d_synth, function(value) 7))
+  assign(paste0(d_synth_name, "_c"), add_err(d_synth,
+                           function(value) sdfunc_twocomp(value, 0.5, 0.07)))
+
+}
+
+d_synth_err_names = c(
+  paste(rep(d_synth_names, each = 3), letters[1:3], sep = "_")
+)
+
+# This is just one example of an evaluation using the kinetic model used for
+# the generation of the data
+fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data,
+               quiet = TRUE)
+plot_sep(fit)
summary(fit)
#> mkin version used for fitting:    0.9.49.6 
+#> R version used for fitting:       3.6.1 
+#> Date of fit:     Thu Sep 19 12:43:02 2019 
+#> Date of summary: Thu Sep 19 12:43:02 2019 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> d_M1/dt = + f_parent_to_M1 * k_parent * parent - k_M1 * M1
+#> d_M2/dt = + f_M1_to_M2 * k_M1 * M1 - k_M2 * M2
+#> 
+#> Model predictions using solution type deSolve 
+#> 
+#> Fitted using 847 model solutions performed in 2.51 s
+#> 
+#> Error model: Constant variance 
+#> 
+#> Error model algorithm: OLS 
+#> 
+#> Starting values for parameters to be optimised:
+#>                     value   type
+#> parent_0       101.350000  state
+#> k_parent         0.100000 deparm
+#> k_M1             0.100100 deparm
+#> k_M2             0.100200 deparm
+#> f_parent_to_M1   0.500000 deparm
+#> f_M1_to_M2       0.500000 deparm
+#> sigma            2.273126  error
+#> 
+#> Starting values for the transformed parameters actually optimised:
+#>                     value lower upper
+#> parent_0       101.350000  -Inf   Inf
+#> log_k_parent    -2.302585  -Inf   Inf
+#> log_k_M1        -2.301586  -Inf   Inf
+#> log_k_M2        -2.300587  -Inf   Inf
+#> f_parent_ilr_1   0.000000  -Inf   Inf
+#> f_M1_ilr_1       0.000000  -Inf   Inf
+#> sigma            2.273126     0   Inf
+#> 
+#> Fixed parameter values:
+#>      value  type
+#> M1_0     0 state
+#> M2_0     0 state
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                Estimate Std. Error   Lower    Upper
+#> parent_0       102.1000    1.57000 98.8600 105.3000
+#> log_k_parent    -0.3020    0.03885 -0.3812  -0.2229
+#> log_k_M1        -1.2070    0.07123 -1.3520  -1.0620
+#> log_k_M2        -3.9010    0.06571 -4.0350  -3.7670
+#> f_parent_ilr_1   0.8492    0.16640  0.5103   1.1880
+#> f_M1_ilr_1       0.6780    0.17600  0.3196   1.0360
+#> sigma            2.2730    0.25740  1.7490   2.7970
+#> 
+#> Parameter correlation:
+#>                  parent_0 log_k_parent   log_k_M1   log_k_M2 f_parent_ilr_1
+#> parent_0        1.000e+00    3.933e-01 -1.605e-01  2.819e-02     -4.624e-01
+#> log_k_parent    3.933e-01    1.000e+00 -4.082e-01  7.166e-02     -5.682e-01
+#> log_k_M1       -1.605e-01   -4.082e-01  1.000e+00 -3.929e-01      7.478e-01
+#> log_k_M2        2.819e-02    7.166e-02 -3.929e-01  1.000e+00     -2.658e-01
+#> f_parent_ilr_1 -4.624e-01   -5.682e-01  7.478e-01 -2.658e-01      1.000e+00
+#> f_M1_ilr_1      1.614e-01    4.102e-01 -8.109e-01  5.419e-01     -8.605e-01
+#> sigma          -3.704e-09   -1.104e-08  5.922e-08 -3.673e-08      5.867e-08
+#>                f_M1_ilr_1      sigma
+#> parent_0        1.614e-01 -3.704e-09
+#> log_k_parent    4.102e-01 -1.104e-08
+#> log_k_M1       -8.109e-01  5.922e-08
+#> log_k_M2        5.419e-01 -3.673e-08
+#> f_parent_ilr_1 -8.605e-01  5.867e-08
+#> f_M1_ilr_1      1.000e+00 -8.075e-08
+#> sigma          -8.075e-08  1.000e+00
+#> 
+#> 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       102.10000  65.000 7.281e-36 98.86000 105.30000
+#> k_parent         0.73930  25.740 2.948e-23  0.68310   0.80020
+#> k_M1             0.29920  14.040 1.577e-15  0.25880   0.34590
+#> k_M2             0.02023  15.220 1.653e-16  0.01769   0.02312
+#> f_parent_to_M1   0.76870  18.370 7.295e-19  0.67300   0.84290
+#> f_M1_to_M2       0.72290  14.500 6.418e-16  0.61110   0.81240
+#> sigma            2.27300   8.832 2.161e-10  1.74900   2.79700
+#> 
+#> FOCUS Chi2 error levels in percent:
+#>          err.min n.optim df
+#> All data   8.454       6 17
+#> parent     8.660       2  6
+#> M1        10.583       2  5
+#> M2         3.586       2  6
+#> 
+#> Resulting formation fractions:
+#>                 ff
+#> parent_M1   0.7687
+#> parent_sink 0.2313
+#> M1_M2       0.7229
+#> M1_sink     0.2771
+#> 
+#> Estimated disappearance times:
+#>           DT50    DT90
+#> parent  0.9376   3.114
+#> M1      2.3170   7.697
+#> M2     34.2689 113.839
+#> 
+#> Data:
+#>  time variable observed  predicted residual
+#>     0   parent    101.5  1.021e+02 -0.56248
+#>     0   parent    101.2  1.021e+02 -0.86248
+#>     1   parent     53.9  4.873e+01  5.17118
+#>     1   parent     47.5  4.873e+01 -1.22882
+#>     3   parent     10.4  1.111e+01 -0.70773
+#>     3   parent      7.6  1.111e+01 -3.50773
+#>     7   parent      1.1  5.772e-01  0.52283
+#>     7   parent      0.3  5.772e-01 -0.27717
+#>    14   parent      3.5  3.264e-03  3.49674
+#>    28   parent      3.2  1.045e-07  3.20000
+#>    90   parent      0.6 -1.875e-11  0.60000
+#>   120   parent      3.5 -2.805e-11  3.50000
+#>     1       M1     36.4  3.479e+01  1.61088
+#>     1       M1     37.4  3.479e+01  2.61088
+#>     3       M1     34.3  3.937e+01 -5.07027
+#>     3       M1     39.8  3.937e+01  0.42973
+#>     7       M1     15.1  1.549e+01 -0.38715
+#>     7       M1     17.8  1.549e+01  2.31285
+#>    14       M1      5.8  1.995e+00  3.80469
+#>    14       M1      1.2  1.995e+00 -0.79531
+#>    60       M1      0.5  2.111e-06  0.50000
+#>    90       M1      3.2  2.913e-10  3.20000
+#>   120       M1      1.5  3.625e-11  1.50000
+#>   120       M1      0.6  3.625e-11  0.60000
+#>     1       M2      4.8  4.455e+00  0.34517
+#>     3       M2     20.9  2.153e+01 -0.62527
+#>     3       M2     19.3  2.153e+01 -2.22527
+#>     7       M2     42.0  4.192e+01  0.07941
+#>     7       M2     43.1  4.192e+01  1.17941
+#>    14       M2     49.4  4.557e+01  3.83353
+#>    14       M2     44.3  4.557e+01 -1.26647
+#>    28       M2     34.6  3.547e+01 -0.87275
+#>    28       M2     33.0  3.547e+01 -2.47275
+#>    60       M2     18.8  1.858e+01  0.21837
+#>    60       M2     17.6  1.858e+01 -0.98163
+#>    90       M2     10.6  1.013e+01  0.47130
+#>    90       M2     10.8  1.013e+01  0.67130
+#>   120       M2      9.8  5.521e+00  4.27893
+#>   120       M2      3.3  5.521e+00 -2.22107
+
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+ + + + + + + + -- cgit v1.2.1