From e5d1df9a9b1f0951d7dfbaf24eee4294470b73e2 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 17 Nov 2022 14:54:20 +0100 Subject: Complete update of online docs for v1.2.0 --- docs/reference/summary.nlme.mmkin.html | 255 +++++++++++++++++++-------------- 1 file changed, 145 insertions(+), 110 deletions(-) (limited to 'docs/reference/summary.nlme.mmkin.html') diff --git a/docs/reference/summary.nlme.mmkin.html b/docs/reference/summary.nlme.mmkin.html index ff014cc1..eb01ef7a 100644 --- a/docs/reference/summary.nlme.mmkin.html +++ b/docs/reference/summary.nlme.mmkin.html @@ -21,7 +21,7 @@ endpoints such as formation fractions and DT50 values. Optionally mkin - 1.1.0 + 1.2.0 @@ -48,11 +48,14 @@ endpoints such as formation fractions and DT50 values. Optionally Example evaluations of dimethenamid data from 2018 with nonlinear mixed-effects models
  • - Example evaluation of FOCUS Example Dataset Z + Short demo of the multistart method
  • Performance benefit by using compiled model definitions in mkin
    • +
  • + Example evaluation of FOCUS Example Dataset Z +
  • Calculation of time weighted average concentrations with mkin
    • @@ -60,7 +63,10 @@ endpoints such as formation fractions and DT50 values. Optionally Example evaluation of NAFTA SOP Attachment examples
  • - Some benchmark timings + Benchmark timings for mkin +
    • +
  • + Benchmark timings for saem.mmkin
  • @@ -95,68 +101,95 @@ endpoints such as formation fractions and DT50 values. Optionally
    - 
    # S3 method for nlme.mmkin
-summary(
-  object,
-  data = FALSE,
-  verbose = FALSE,
-  distimes = TRUE,
-  alpha = 0.05,
-  ...
-)
-
-# S3 method for summary.nlme.mmkin
-print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)
    + 
    # S3 method for nlme.mmkin
+summary(
+  object,
+  data = FALSE,
+  verbose = FALSE,
+  distimes = TRUE,
+  alpha = 0.05,
+  ...
+)
+
+# S3 method for summary.nlme.mmkin
+print(x, digits = max(3, getOption("digits") - 3), verbose = x$verbose, ...)

    Arguments

    object

    an object of class nlme.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.

    + +
    alpha

    error level for confidence interval estimation from the t distribution

    + +
    ...

    optional arguments passed to methods like print.

    + +
    x

    an object of class summary.nlme.mmkin

    + +
    digits

    Number of digits to use for printing

    +

    Value

    -

    The summary function returns a list based on the nlme object + + +

    The summary function returns a list based on the nlme object obtained in the fit, with at least the following additional components

    nlmeversion, mkinversion, Rversion

    The nlme, 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

    +
    ff

    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.

    @@ -167,44 +200,46 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

    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)
-
-set.seed(12345)
-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 nlme
-library(nlme)
-f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
-f_nlme <- nlme(f_mmkin)
+    
    
+# 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)
+
+set.seed(12345)
+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 nlme
+library(nlme)
+f_mmkin <- mmkin("SFO", ds_sfo_syn, quiet = TRUE, error_model = "tc", cores = 1)
+#> Warning: Optimisation did not converge:
+#> iteration limit reached without convergence (10)
+f_nlme <- nlme(f_mmkin)
 #> Warning: Iteration 4, LME step: nlminb() did not converge (code = 1). PORT message: false convergence (8)
-summary(f_nlme, data = TRUE)
-#> nlme version used for fitting:      3.1.155 
-#> mkin version used for pre-fitting:  1.1.0 
-#> R version used for fitting:         4.2.1 
-#> Date of fit:     Thu Jun 30 10:23:57 2022 
-#> Date of summary: Thu Jun 30 10:23:57 2022 
+summary(f_nlme, data = TRUE)
+#> nlme version used for fitting:      3.1.160 
+#> mkin version used for pre-fitting:  1.2.0 
+#> R version used for fitting:         4.2.2 
+#> Date of fit:     Thu Nov 17 14:03:27 2022 
+#> Date of summary: Thu Nov 17 14:03:27 2022 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -220,7 +255,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
    
 #> 
 #> Mean of starting values for individual parameters:
 #>     parent_0 log_k_parent 
-#>      101.612       -4.454 
+#>      101.569       -4.454 
 #> 
 #> Fixed degradation parameter values:
 #> None
@@ -244,18 +279,18 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
    
 #>  Level: ds
 #>  Structure: Diagonal
 #>          parent_0 log_k_parent Residual
-#> StdDev: 6.904e-05       0.5863        1
+#> StdDev: 6.924e-05       0.5863        1
 #> 
 #> Variance function:
 #>  Structure: Constant plus proportion of variance covariate
 #>  Formula: ~fitted(.) 
 #>  Parameter estimates:
-#>       const        prop 
-#> 0.000121099 0.078996777 
+#>        const         prop 
+#> 0.0001208853 0.0789968036 
 #> 
 #> Backtransformed parameters with asymmetric confidence intervals:
 #>              lower      est.     upper
-#> parent_0 99.370886 101.59243 103.81398
+#> parent_0 99.370882 101.59243 103.81398
 #> k_parent  0.006923   0.01168   0.01972
 #> 
 #> Estimated disappearance times:
@@ -266,48 +301,48 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
    
 #>    ds   name time observed predicted  residual    std standardized
 #>  ds 1 parent    0    104.1   101.592   2.50757 8.0255     0.312451
 #>  ds 1 parent    0    105.0   101.592   3.40757 8.0255     0.424594
-#>  ds 1 parent    1     98.5   100.796  -2.29571 7.9625    -0.288314
+#>  ds 1 parent    1     98.5   100.796  -2.29571 7.9625    -0.288313
 #>  ds 1 parent    1     96.1   100.796  -4.69571 7.9625    -0.589725
 #>  ds 1 parent    3    101.9    99.221   2.67904 7.8381     0.341796
-#>  ds 1 parent    3     85.2    99.221 -14.02096 7.8381    -1.788813
-#>  ds 1 parent    7     99.1    96.145   2.95512 7.5951     0.389080
+#>  ds 1 parent    3     85.2    99.221 -14.02096 7.8381    -1.788812
+#>  ds 1 parent    7     99.1    96.145   2.95512 7.5951     0.389081
 #>  ds 1 parent    7     93.0    96.145  -3.14488 7.5951    -0.414065
-#>  ds 1 parent   14     88.1    90.989  -2.88944 7.1879    -0.401988
-#>  ds 1 parent   14     84.1    90.989  -6.88944 7.1879    -0.958481
+#>  ds 1 parent   14     88.1    90.989  -2.88944 7.1879    -0.401987
+#>  ds 1 parent   14     84.1    90.989  -6.88944 7.1879    -0.958480
 #>  ds 1 parent   28     80.2    81.493  -1.29305 6.4377    -0.200857
 #>  ds 1 parent   28     91.3    81.493   9.80695 6.4377     1.523364
 #>  ds 1 parent   60     65.1    63.344   1.75642 5.0039     0.351008
 #>  ds 1 parent   60     65.8    63.344   2.45642 5.0039     0.490898
-#>  ds 1 parent   90     47.8    50.018  -2.21764 3.9512    -0.561253
+#>  ds 1 parent   90     47.8    50.018  -2.21764 3.9512    -0.561252
 #>  ds 1 parent   90     53.5    50.018   3.48236 3.9512     0.881335
 #>  ds 1 parent  120     37.6    39.495  -1.89515 3.1200    -0.607423
 #>  ds 1 parent  120     39.3    39.495  -0.19515 3.1200    -0.062549
 #>  ds 2 parent    0    107.9   101.592   6.30757 8.0255     0.785943
-#>  ds 2 parent    0    102.1   101.592   0.50757 8.0255     0.063244
+#>  ds 2 parent    0    102.1   101.592   0.50757 8.0255     0.063245
 #>  ds 2 parent    1    103.8   100.058   3.74159 7.9043     0.473361
 #>  ds 2 parent    1    108.6   100.058   8.54159 7.9043     1.080626
 #>  ds 2 parent    3     91.0    97.060  -6.05952 7.6674    -0.790297
-#>  ds 2 parent    3     84.9    97.060 -12.15952 7.6674    -1.585875
-#>  ds 2 parent    7     79.3    91.329 -12.02867 7.2147    -1.667252
+#>  ds 2 parent    3     84.9    97.060 -12.15952 7.6674    -1.585874
+#>  ds 2 parent    7     79.3    91.329 -12.02867 7.2147    -1.667251
 #>  ds 2 parent    7    100.9    91.329   9.57133 7.2147     1.326647
 #>  ds 2 parent   14     77.3    82.102  -4.80185 6.4858    -0.740366
 #>  ds 2 parent   14     83.5    82.102   1.39815 6.4858     0.215571
 #>  ds 2 parent   28     66.8    66.351   0.44945 5.2415     0.085748
 #>  ds 2 parent   28     63.3    66.351  -3.05055 5.2415    -0.582002
-#>  ds 2 parent   60     40.8    40.775   0.02474 3.2211     0.007681
-#>  ds 2 parent   60     44.8    40.775   4.02474 3.2211     1.249487
-#>  ds 2 parent   90     27.8    25.832   1.96762 2.0407     0.964200
-#>  ds 2 parent   90     27.0    25.832   1.16762 2.0407     0.572173
-#>  ds 2 parent  120     15.2    16.366  -1.16561 1.2928    -0.901593
-#>  ds 2 parent  120     15.5    16.366  -0.86561 1.2928    -0.669544
-#>  ds 3 parent    0     97.7   101.592  -3.89243 8.0255    -0.485010
-#>  ds 3 parent    0     88.2   101.592 -13.39243 8.0255    -1.668740
-#>  ds 3 parent    1    109.9    99.218  10.68195 7.8379     1.362858
-#>  ds 3 parent    1     97.8    99.218  -1.41805 7.8379    -0.180921
+#>  ds 2 parent   60     40.8    40.775   0.02474 3.2211     0.007679
+#>  ds 2 parent   60     44.8    40.775   4.02474 3.2211     1.249485
+#>  ds 2 parent   90     27.8    25.832   1.96762 2.0407     0.964198
+#>  ds 2 parent   90     27.0    25.832   1.16762 2.0407     0.572171
+#>  ds 2 parent  120     15.2    16.366  -1.16561 1.2928    -0.901595
+#>  ds 2 parent  120     15.5    16.366  -0.86561 1.2928    -0.669547
+#>  ds 3 parent    0     97.7   101.592  -3.89243 8.0255    -0.485009
+#>  ds 3 parent    0     88.2   101.592 -13.39243 8.0255    -1.668739
+#>  ds 3 parent    1    109.9    99.218  10.68196 7.8379     1.362858
+#>  ds 3 parent    1     97.8    99.218  -1.41804 7.8379    -0.180921
 #>  ds 3 parent    3    100.5    94.634   5.86555 7.4758     0.784603
-#>  ds 3 parent    3     77.4    94.634 -17.23445 7.4758    -2.305361
-#>  ds 3 parent    7     78.3    86.093  -7.79273 6.8010    -1.145814
-#>  ds 3 parent    7     90.3    86.093   4.20727 6.8010     0.618620
+#>  ds 3 parent    3     77.4    94.634 -17.23445 7.4758    -2.305360
+#>  ds 3 parent    7     78.3    86.093  -7.79273 6.8011    -1.145813
+#>  ds 3 parent    7     90.3    86.093   4.20727 6.8011     0.618620
 #>  ds 3 parent   14     76.0    72.958   3.04222 5.7634     0.527848
 #>  ds 3 parent   14     79.1    72.958   6.14222 5.7634     1.065722
 #>  ds 3 parent   28     46.0    52.394  -6.39404 4.1390    -1.544842
@@ -315,47 +350,47 @@ José Pinheiro and Douglas Bates for the components inherited from nlme
    
 #>  ds 3 parent   60     25.1    24.582   0.51786 1.9419     0.266676
 #>  ds 3 parent   60     21.4    24.582  -3.18214 1.9419    -1.638664
 #>  ds 3 parent   90     11.0    12.092  -1.09202 0.9552    -1.143199
-#>  ds 3 parent   90     14.2    12.092   2.10798 0.9552     2.206778
+#>  ds 3 parent   90     14.2    12.092   2.10798 0.9552     2.206776
 #>  ds 3 parent  120      5.8     5.948  -0.14810 0.4699    -0.315178
-#>  ds 3 parent  120      6.1     5.948   0.15190 0.4699     0.323283
+#>  ds 3 parent  120      6.1     5.948   0.15190 0.4699     0.323282
 #>  ds 4 parent    0     95.3   101.592  -6.29243 8.0255    -0.784057
 #>  ds 4 parent    0    102.0   101.592   0.40757 8.0255     0.050784
 #>  ds 4 parent    1    104.4   101.125   3.27549 7.9885     0.410025
-#>  ds 4 parent    1    105.4   101.125   4.27549 7.9885     0.535204
+#>  ds 4 parent    1    105.4   101.125   4.27549 7.9885     0.535205
 #>  ds 4 parent    3    113.7   100.195  13.50487 7.9151     1.706218
-#>  ds 4 parent    3     82.3   100.195 -17.89513 7.9151    -2.260887
-#>  ds 4 parent    7     98.1    98.362  -0.26191 7.7703    -0.033706
-#>  ds 4 parent    7     87.8    98.362 -10.56191 7.7703    -1.359271
-#>  ds 4 parent   14     97.9    95.234   2.66589 7.5232     0.354356
-#>  ds 4 parent   14    104.8    95.234   9.56589 7.5232     1.271521
-#>  ds 4 parent   28     85.0    89.274  -4.27373 7.0523    -0.606002
-#>  ds 4 parent   28     77.2    89.274 -12.07373 7.0523    -1.712019
-#>  ds 4 parent   60     82.2    77.013   5.18659 6.0838     0.852523
-#>  ds 4 parent   60     86.1    77.013   9.08659 6.0838     1.493568
-#>  ds 4 parent   90     70.5    67.053   3.44690 5.2970     0.650729
-#>  ds 4 parent   90     61.7    67.053  -5.35310 5.2970    -1.010595
-#>  ds 4 parent  120     60.0    58.381   1.61902 4.6119     0.351052
-#>  ds 4 parent  120     56.4    58.381  -1.98098 4.6119    -0.429535
-#>  ds 5 parent    0     92.6   101.592  -8.99243 8.0255    -1.120486
+#>  ds 4 parent    3     82.3   100.195 -17.89513 7.9151    -2.260886
+#>  ds 4 parent    7     98.1    98.362  -0.26190 7.7703    -0.033706
+#>  ds 4 parent    7     87.8    98.362 -10.56190 7.7703    -1.359270
+#>  ds 4 parent   14     97.9    95.234   2.66590 7.5232     0.354357
+#>  ds 4 parent   14    104.8    95.234   9.56590 7.5232     1.271521
+#>  ds 4 parent   28     85.0    89.274  -4.27372 7.0523    -0.606001
+#>  ds 4 parent   28     77.2    89.274 -12.07372 7.0523    -1.712017
+#>  ds 4 parent   60     82.2    77.013   5.18661 6.0838     0.852526
+#>  ds 4 parent   60     86.1    77.013   9.08661 6.0838     1.493571
+#>  ds 4 parent   90     70.5    67.053   3.44692 5.2970     0.650733
+#>  ds 4 parent   90     61.7    67.053  -5.35308 5.2970    -1.010591
+#>  ds 4 parent  120     60.0    58.381   1.61905 4.6119     0.351058
+#>  ds 4 parent  120     56.4    58.381  -1.98095 4.6119    -0.429530
+#>  ds 5 parent    0     92.6   101.592  -8.99243 8.0255    -1.120485
 #>  ds 5 parent    0    116.5   101.592  14.90757 8.0255     1.857531
-#>  ds 5 parent    1    108.0    99.914   8.08560 7.8929     1.024412
+#>  ds 5 parent    1    108.0    99.914   8.08560 7.8929     1.024413
 #>  ds 5 parent    1    104.9    99.914   4.98560 7.8929     0.631655
 #>  ds 5 parent    3    100.5    96.641   3.85898 7.6343     0.505477
-#>  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935383
+#>  ds 5 parent    3     89.5    96.641  -7.14102 7.6343    -0.935382
 #>  ds 5 parent    7     91.7    90.412   1.28752 7.1423     0.180267
 #>  ds 5 parent    7     95.1    90.412   4.68752 7.1423     0.656304
-#>  ds 5 parent   14     82.2    80.463   1.73715 6.3563     0.273296
+#>  ds 5 parent   14     82.2    80.463   1.73715 6.3563     0.273295
 #>  ds 5 parent   14     84.5    80.463   4.03715 6.3563     0.635141
 #>  ds 5 parent   28     60.5    63.728  -3.22788 5.0343    -0.641178
-#>  ds 5 parent   28     72.8    63.728   9.07212 5.0343     1.802063
-#>  ds 5 parent   60     38.3    37.399   0.90062 2.9544     0.304836
-#>  ds 5 parent   60     40.7    37.399   3.30062 2.9544     1.117176
-#>  ds 5 parent   90     22.5    22.692  -0.19164 1.7926    -0.106910
-#>  ds 5 parent   90     20.8    22.692  -1.89164 1.7926    -1.055271
-#>  ds 5 parent  120     13.4    13.768  -0.36789 1.0876    -0.338255
-#>  ds 5 parent  120     13.8    13.768   0.03211 1.0876     0.029520
-# }
-
+#>  ds 5 parent   28     72.8    63.728   9.07212 5.0343     1.802062
+#>  ds 5 parent   60     38.3    37.399   0.90061 2.9544     0.304835
+#>  ds 5 parent   60     40.7    37.399   3.30061 2.9544     1.117174
+#>  ds 5 parent   90     22.5    22.692  -0.19165 1.7926    -0.106913
+#>  ds 5 parent   90     20.8    22.692  -1.89165 1.7926    -1.055273
+#>  ds 5 parent  120     13.4    13.768  -0.36790 1.0876    -0.338259
+#>  ds 5 parent  120     13.8    13.768   0.03210 1.0876     0.029517
+# }
+
    @@ -370,7 +405,7 @@ José Pinheiro and Douglas Bates for the components inherited from nlme

    -

    Site built with pkgdown 2.0.3.

    +

    Site built with pkgdown 2.0.6.

    -- cgit v1.2.1