Summary method for class "saem.mmkin"

Author

Johannes Ranke

Fit nonlinear mixed models with SAEM

This function uses saemix::saemix() as a backend for fitting nonlinear mixed -effects models created from mmkin row objects using the stochastic approximation -to the expectation maximisation algorithm (SAEM).

+effects models created from mmkin row objects using the Stochastic Approximation +Expectation Maximisation algorithm (SAEM).

saem(object, control, ...) @@ -205,7 +205,8 @@ by the saemix function?

Value

An saemix::SaemixObject.

An S3 object of class 'saem.mmkin', containing the fitted +saemix::SaemixObject as a list component named 'so'.

An saemix::SaemixModel object.

An saemix::SaemixData object.

Details

@@ -215,6 +216,9 @@ obtained by fitting the same model to a list of datasets using saemix::saemixModel() are the mean values of the parameters found using mmkin.

Examples

# \dontrun{
@@ -225,27 +229,27 @@ using mmkin.
   state.ini = c(parent = 100), fixed_initials = "parent", quiet = TRUE)
 f_saem_p0_fixed <- saem(f_mmkin_parent_p0_fixed)
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:14:50 2020"
+#> [1] "Sun Nov  8 02:44:42 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:14:52 2020"

+#> [1] "Sun Nov  8 02:44:43 2020"

 f_mmkin_parent <- mmkin(c("SFO", "FOMC", "DFOP"), ds, quiet = TRUE)
 f_saem_sfo <- saem(f_mmkin_parent["SFO", ])
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:14:53 2020"
+#> [1] "Sun Nov  8 02:44:45 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:14:55 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
+#> [1] "Sun Nov  8 02:44:46 2020"
f_saem_fomc <- saem(f_mmkin_parent["FOMC", ])
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:14:55 2020"
+#> [1] "Sun Nov  8 02:44:47 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:14:57 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
+#> [1] "Sun Nov  8 02:44:49 2020"
f_saem_dfop <- saem(f_mmkin_parent["DFOP", ])
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:14:57 2020"
+#> [1] "Sun Nov  8 02:44:49 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:15:00 2020"

+#> [1] "Sun Nov  8 02:44:52 2020"

 # The returned saem.mmkin object contains an SaemixObject, we can use
 # functions from saemix
 library(saemix)
@@ -258,10 +262,10 @@ using mmkin.
 f_mmkin_parent_tc <- update(f_mmkin_parent, error_model = "tc")
 f_saem_fomc_tc <- saem(f_mmkin_parent_tc["FOMC", ])
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:15:02 2020"
+#> [1] "Sun Nov  8 02:44:54 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:15:07 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
+#> [1] "Sun Nov  8 02:44:59 2020"
compare.saemix(list(f_saem_fomc$so, f_saem_fomc_tc$so))
 
#> Likelihoods computed by importance sampling 
#>        AIC      BIC
 #> 1 467.7644 465.0305
 #> 2 469.4862 466.3617

@@ -271,20 +275,20 @@ using mmkin.
 # This takes about 4 minutes on my system
 f_saem <- saem(f_mmkin)
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:15:08 2020"
+#> [1] "Sun Nov  8 02:45:00 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:19:07 2020"

+#> [1] "Sun Nov  8 02:49:01 2020"
#> Error in exp(trans_k): non-numeric argument to mathematical function
#> Timing stopped at: 317.7 169.9 258.9

 f_mmkin_des <- mmkin(list("DFOP-SFO" = dfop_sfo), ds, quiet = TRUE, solution_type = "deSolve")
 # Using a single core, the following takes about 6 minutes, using 10 cores
 # it is slower instead of faster
 f_saem_des <- saem(f_mmkin_des, cores = 1)
 
#> Running main SAEM algorithm
-#> [1] "Sat Nov  7 13:19:26 2020"
+#> [1] "Sun Nov  8 02:49:20 2020"
 #> ....
 #>     Minimisation finished
-#> [1] "Sat Nov  7 13:27:33 2020"
compare.saemix(list(f_saemix$so, f_saemix_des$so))
-
#> Error in compare.saemix(list(f_saemix$so, f_saemix_des$so)): object 'f_saemix' not found
# }
+#> [1] "Sun Nov  8 02:57:30 2020"
#> Error in exp(trans_k): non-numeric argument to mathematical function
#> Timing stopped at: 591.7 205.6 521.4
compare.saemix(list(f_saem$so, f_saem_des$so))
+
#> Error in compare.saemix(list(f_saem$so, f_saem_des$so)): object 'f_saem' not found
# }

diff --git a/docs/dev/reference/summary.saem.mmkin.html b/docs/dev/reference/summary.saem.mmkin.html new file mode 100644 index 00000000..01e8eb12 --- /dev/null +++ b/docs/dev/reference/summary.saem.mmkin.html @@ -0,0 +1,436 @@ + + + + + + + + +Summary method for class "saem.mmkin" — summary.saem.mmkin • mkin + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

+ + + + +

+ +

+ + +

Lists model equations, initial parameter values, optimised parameters +for fixed effects (population), random effects (deviations from the +population mean) and residual error model, as well as the resulting +endpoints such as formation fractions and DT50 values. Optionally +(default is FALSE), the data are listed in full.

+ +

# S3 method for saem.mmkin
+summary(object, data = FALSE, verbose = FALSE, distimes = TRUE, ...)
+
+# S3 method for summary.saem.mmkin
+print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)

+ +

Arguments

+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +

object	an object of class saem.mmkin
data	logical, indicating whether the full data should be included in +the summary.
verbose	Should the summary be verbose?
distimes	logical, indicating whether DT50 and DT90 values should be +included.
...	optional arguments passed to methods like `print`.
x	an object of class summary.saem.mmkin
digits	Number of digits to use for printing

+ +

Value

+ +

The summary function returns a list based on the saemix::SaemixObject +obtained in the fit, with at least the following additional components

saemixversion, mkinversion, Rversion

The saemix, mkin and R versions used

date.fit, date.summary

The dates where the fit and the summary were +produced

diffs

The differential equations used in the degradation model

use_of_ff

Was maximum or minimum use made of formation fractions

data

The data

confint_trans

Transformed parameters as used in the optimisation, with confidence intervals

confint_back

Backtransformed parameters, with confidence intervals if available

The estimated formation fractions derived from the fitted +model.

distimes

The DT50 and DT90 values for each observed variable.

SFORB

If applicable, eigenvalues of SFORB components of the model.

+The print method is called for its side effect, i.e. printing the summary. + +

Author

+ +

Johannes Ranke for the mkin specific parts +saemix authors for the parts inherited from saemix.

+ +

Examples

# Generate five datasets following SFO kinetics
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+dt50_sfo_in_pop <- 50
+k_in_pop <- log(2) / dt50_sfo_in_pop
+set.seed(1234)
+k_in <- rlnorm(5, log(k_in_pop), 0.5)
+SFO <- mkinmod(parent = mkinsub("SFO"))
+
+pred_sfo <- function(k) {
+  mkinpredict(SFO,
+    c(k_parent = k),
+    c(parent = 100),
+    sampling_times)
+}
+
+ds_sfo_mean <- lapply(k_in, pred_sfo)
+names(ds_sfo_mean) <- paste("ds", 1:5)
+
+ds_sfo_syn <- lapply(ds_sfo_mean, function(ds) {
+  add_err(ds,
+    sdfunc = function(value) sqrt(1^2 + value^2 * 0.07^2),
+    n = 1)[[1]]
+})
+
+# \dontrun{
+# Evaluate using mmkin and saem
+f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
+f_saem <- saem(f_mmkin)
+
#> Running main SAEM algorithm
+#> [1] "Sun Nov  8 02:58:03 2020"
+#> ....
+#>     Minimisation finished
+#> [1] "Sun Nov  8 02:58:07 2020"
summary(f_saem, data = TRUE)
+
#> saemix version used for fitting:      3.1.9000 
+#> mkin version used for pre-fitting:  0.9.50.4 
+#> R version used for fitting:         4.0.3 
+#> Date of fit:     Sun Nov  8 02:58:07 2020 
+#> Date of summary: Sun Nov  8 02:58:07 2020 
+#> 
+#> Equations:
+#> d_parent/dt = - k_parent * parent
+#> 
+#> Data:
+#> 90 observations of 1 variable(s) grouped in 5 datasets
+#> 
+#> Model predictions using solution type analytical 
+#> 
+#> Fitted in 4.175 s using 300, 100 iterations
+#> 
+#> Variance model: Two-component variance function 
+#> 
+#> Mean of starting values for individual parameters:
+#>     parent_0 log_k_parent 
+#>    97.849556    -4.455036 
+#> 
+#> Fixed degradation parameter values:
+#> None
+#> 
+#> Results:
+#> 
+#> Likelihood computed by importance sampling
+#>        AIC      BIC    logLik
+#>   555.6718 553.3284 -271.8359
+#> 
+#> Optimised, transformed parameters with symmetric confidence intervals:
+#>                   est.     lower      upper
+#> parent_0     97.840291 94.701895 100.978686
+#> log_k_parent -4.464246 -5.001413  -3.927078
+#> 
+#> Correlation: 
+#>              prnt_0
+#> log_k_parent 0.022 
+#> 
+#> Random effects:
+#>                      est.     lower     upper
+#> SD.parent_0     3.0805465 0.4960170 5.6650760
+#> SD.log_k_parent 0.6109508 0.2301398 0.9917617
+#> 
+#> Variance model:
+#>           est.      lower      upper
+#> a.1 1.06249961 0.23012265 1.89487657
+#> b.1 0.04649661 0.03060849 0.06238473
+#> 
+#> Backtransformed parameters with asymmetric confidence intervals:
+#>                 est.        lower        upper
+#> parent_0 97.84029088 94.701895315 100.97868644
+#> k_parent  0.01151338  0.006728434   0.01970115
+#> 
+#> Estimated disappearance times:
+#>        DT50 DT90
+#> parent 60.2  200
+#> 
+#> Data:
+#>    ds   name time observed predicted   residual standardized
+#>  ds 1 parent    0    103.6    97.303   6.297361     -1.12720
+#>  ds 1 parent    0     95.9    97.303  -1.402639      0.25107
+#>  ds 1 parent    1     95.4    96.599  -1.198705      0.21583
+#>  ds 1 parent    1     95.3    96.599  -1.298705      0.23383
+#>  ds 1 parent    3     91.6    95.206  -3.606076      0.65693
+#>  ds 1 parent    3     94.5    95.206  -0.706076      0.12863
+#>  ds 1 parent    7     88.1    92.481  -4.380761      0.81692
+#>  ds 1 parent    7     89.6    92.481  -2.880761      0.53720
+#>  ds 1 parent   14     90.3    87.898   2.402166     -0.46649
+#>  ds 1 parent   14     96.0    87.898   8.102166     -1.57340
+#>  ds 1 parent   28     80.2    79.402   0.797948     -0.16783
+#>  ds 1 parent   28     77.9    79.402  -1.502052      0.31593
+#>  ds 1 parent   60     59.3    62.940  -3.639829      0.91247
+#>  ds 1 parent   60     59.6    62.940  -3.339829      0.83726
+#>  ds 1 parent   90     59.4    50.620   8.779547     -2.56999
+#>  ds 1 parent   90     51.0    50.620   0.379547     -0.11110
+#>  ds 1 parent  120     38.8    40.712  -1.912380      0.64706
+#>  ds 1 parent  120     38.9    40.712  -1.812380      0.61323
+#>  ds 2 parent    0    103.2    97.185   6.015158     -1.07774
+#>  ds 2 parent    0     95.1    97.185  -2.084842      0.37354
+#>  ds 2 parent    1     88.3    95.609  -7.309466      1.32706
+#>  ds 2 parent    1    102.4    95.609   6.790534     -1.23285
+#>  ds 2 parent    3     88.4    92.535  -4.134911      0.77071
+#>  ds 2 parent    3     95.2    92.535   2.665089     -0.49675
+#>  ds 2 parent    7     83.5    86.679  -3.179231      0.62426
+#>  ds 2 parent    7     96.4    86.679   9.720769     -1.90873
+#>  ds 2 parent   14     77.3    77.309  -0.009268      0.00199
+#>  ds 2 parent   14     76.0    77.309  -1.309268      0.28113
+#>  ds 2 parent   28     61.7    61.499   0.201491     -0.05137
+#>  ds 2 parent   28     56.5    61.499  -4.998509      1.27449
+#>  ds 2 parent   60     35.1    36.454  -1.353571      0.49087
+#>  ds 2 parent   60     32.2    36.454  -4.253571      1.54256
+#>  ds 2 parent   90     21.2    22.326  -1.125996      0.53604
+#>  ds 2 parent   90     23.3    22.326   0.974004     -0.46368
+#>  ds 2 parent  120     14.1    13.674   0.426440     -0.25110
+#>  ds 2 parent  120     16.9    13.674   3.226440     -1.89983
+#>  ds 3 parent    0     92.4    93.838  -1.437848      0.26501
+#>  ds 3 parent    0     94.0    93.838   0.162152     -0.02989
+#>  ds 3 parent    1     95.7    91.709   3.991384     -0.74932
+#>  ds 3 parent    1     90.8    91.709  -0.908616      0.17058
+#>  ds 3 parent    3     86.7    87.594  -0.893997      0.17409
+#>  ds 3 parent    3     85.8    87.594  -1.793997      0.34934
+#>  ds 3 parent    7     77.1    79.910  -2.810299      0.58817
+#>  ds 3 parent    7     81.5    79.910   1.589701     -0.33271
+#>  ds 3 parent   14     69.1    68.050   1.050102     -0.24845
+#>  ds 3 parent   14     62.4    68.050  -5.649898      1.33675
+#>  ds 3 parent   28     49.1    49.349  -0.248837      0.07412
+#>  ds 3 parent   28     47.2    49.349  -2.148837      0.64010
+#>  ds 3 parent   60     21.9    23.676  -1.775776      0.82085
+#>  ds 3 parent   60     23.6    23.676  -0.075776      0.03503
+#>  ds 3 parent   90     12.4    11.892   0.507660     -0.31425
+#>  ds 3 parent   90     13.8    11.892   1.907660     -1.18088
+#>  ds 3 parent  120      4.9     5.974  -1.073521      0.80099
+#>  ds 3 parent  120      7.5     5.974   1.526479     -1.13895
+#>  ds 4 parent    0     91.8   102.087 -10.287197      1.77084
+#>  ds 4 parent    0    104.6   102.087   2.512803     -0.43256
+#>  ds 4 parent    1    117.5   101.632  15.867689     -2.74145
+#>  ds 4 parent    1     99.3   101.632  -2.332311      0.40295
+#>  ds 4 parent    3     94.0   100.729  -6.728610      1.17100
+#>  ds 4 parent    3     98.7   100.729  -2.028610      0.35304
+#>  ds 4 parent    7    109.2    98.945  10.254756     -1.81080
+#>  ds 4 parent    7     89.2    98.945  -9.745244      1.72083
+#>  ds 4 parent   14    103.3    95.900   7.400009     -1.34021
+#>  ds 4 parent   14    103.0    95.900   7.100009     -1.28588
+#>  ds 4 parent   28     90.8    90.088   0.712227     -0.13563
+#>  ds 4 parent   28     88.7    90.088  -1.387773      0.26427
+#>  ds 4 parent   60     74.8    78.091  -3.291273      0.70124
+#>  ds 4 parent   60     75.3    78.091  -2.791273      0.59471
+#>  ds 4 parent   90     71.1    68.300   2.800407     -0.66075
+#>  ds 4 parent   90     78.0    68.300   9.700407     -2.28880
+#>  ds 4 parent  120     59.1    59.736  -0.635668      0.16554
+#>  ds 4 parent  120     53.8    59.736  -5.935668      1.54574
+#>  ds 5 parent    0     94.9    98.353  -3.452694      0.61266
+#>  ds 5 parent    0    101.8    98.353   3.447306     -0.61171
+#>  ds 5 parent    1     96.1    96.722  -0.621996      0.11187
+#>  ds 5 parent    1     97.1    96.722   0.378004     -0.06799
+#>  ds 5 parent    3     93.8    93.541   0.258738     -0.04781
+#>  ds 5 parent    3     85.8    93.541  -7.741262      1.43043
+#>  ds 5 parent    7     87.6    87.490   0.109848     -0.02141
+#>  ds 5 parent    7     94.0    87.490   6.509848     -1.26885
+#>  ds 5 parent   14     82.5    77.827   4.672679     -0.99818
+#>  ds 5 parent   14     81.7    77.827   3.872679     -0.82728
+#>  ds 5 parent   28     60.0    61.585  -1.585419      0.40382
+#>  ds 5 parent   28     61.0    61.585  -0.585419      0.14911
+#>  ds 5 parent   60     32.5    36.068  -3.568284      1.30251
+#>  ds 5 parent   60     35.5    36.068  -0.568284      0.20744
+#>  ds 5 parent   90     21.8    21.842  -0.042136      0.02028
+#>  ds 5 parent   90     24.4    21.842   2.557864     -1.23088
+#>  ds 5 parent  120     14.1    13.227   0.872898     -0.52035
+#>  ds 5 parent  120     12.1    13.227  -1.127102      0.67189
# }
+
+

+ +

+ + + +

+ + + + + + + + diff --git a/docs/dev/sitemap.xml b/docs/dev/sitemap.xml index c5f285f1..d9ef2228 100644 --- a/docs/dev/sitemap.xml +++ b/docs/dev/sitemap.xml @@ -189,6 +189,9 @@ https://pkgdown.jrwb.de/mkin/reference/summary.nlme.mmkin.html + + https://pkgdown.jrwb.de/mkin/reference/summary.saem.mmkin.html + https://pkgdown.jrwb.de/mkin/reference/synthetic_data_for_UBA_2014.html -- cgit v1.2.1

Details

Note

Author

Value

Details

See also

Examples

Arguments

Value

Author

Examples