From 630e657f1794ea441afc9ff10663309fec5e847e Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 1 Nov 2022 14:16:21 +0100 Subject: Update online docs --- docs/dev/articles/index.html | 2 +- docs/dev/articles/web_only/benchmarks.html | 38 +++++- docs/dev/articles/web_only/compiled_models.html | 168 +++++++++++++----------- docs/dev/articles/web_only/multistart.html | 16 +-- docs/dev/authors.html | 6 +- docs/dev/index.html | 2 +- docs/dev/news/index.html | 15 ++- docs/dev/pkgdown.yml | 2 +- docs/dev/reference/Rplot001.png | Bin 20021 -> 1011 bytes docs/dev/reference/Rplot002.png | Bin 17243 -> 17010 bytes docs/dev/reference/anova.saem.mmkin.html | 14 +- docs/dev/reference/aw.html | 7 +- docs/dev/reference/illparms.html | 21 ++- docs/dev/reference/index.html | 4 +- docs/dev/reference/llhist.html | 2 +- docs/dev/reference/logLik.saem.mmkin.html | 2 +- docs/dev/reference/mhmkin.html | 14 +- docs/dev/reference/mkinfit.html | 33 ++--- docs/dev/reference/multistart.html | 3 +- docs/dev/reference/parms.html | 2 +- docs/dev/reference/parplot.html | 2 +- docs/dev/reference/plot.mixed.mmkin-4.png | Bin 175535 -> 175586 bytes docs/dev/reference/plot.mixed.mmkin.html | 14 +- docs/dev/reference/saem.html | 18 ++- docs/dev/reference/set_nd_nq.html | 2 +- docs/dev/reference/status.html | 2 +- docs/dev/reference/summary.mkinfit.html | 15 ++- docs/dev/reference/summary.mmkin.html | 8 +- docs/dev/reference/summary.saem.mmkin.html | 39 +++--- vignettes/web_only/mkin_benchmarks.rda | Bin 1536 -> 1589 bytes 30 files changed, 275 insertions(+), 176 deletions(-) diff --git a/docs/dev/articles/index.html b/docs/dev/articles/index.html index 551e9c98..45ba1c77 100644 --- a/docs/dev/articles/index.html +++ b/docs/dev/articles/index.html @@ -17,7 +17,7 @@ mkin - 1.1.2 + 1.2.0 diff --git a/docs/dev/articles/web_only/benchmarks.html b/docs/dev/articles/web_only/benchmarks.html index e5bc5a21..2aa2f45a 100644 --- a/docs/dev/articles/web_only/benchmarks.html +++ b/docs/dev/articles/web_only/benchmarks.html @@ -34,7 +34,7 @@ mkin - 1.1.2 + 1.2.0 @@ -63,11 +63,14 @@ 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
  • @@ -106,7 +109,7 @@

    Benchmark timings for mkin

    Johannes Ranke

    -

    Last change 14 July 2022 (rebuilt 2022-09-16)

    +

    Last change 14 July 2022 (rebuilt 2022-11-01)

    Source: vignettes/web_only/benchmarks.rmd @@ -340,6 +343,14 @@ 1.957 3.633 + +Linux +Ryzen 7 1700 +4.2.2 +1.2.0 +2.020 +3.608 + @@ -511,6 +522,15 @@ 6.147 2.803 + +Linux +Ryzen 7 1700 +4.2.2 +1.2.0 +1.579 +5.973 +2.839 + @@ -736,6 +756,18 @@ 1.961 2.852 + +Linux +Ryzen 7 1700 +4.2.2 +1.2.0 +0.920 +1.295 +1.518 +3.060 +1.895 +2.740 + diff --git a/docs/dev/articles/web_only/compiled_models.html b/docs/dev/articles/web_only/compiled_models.html index 49a579fc..ade86bc5 100644 --- a/docs/dev/articles/web_only/compiled_models.html +++ b/docs/dev/articles/web_only/compiled_models.html @@ -20,6 +20,8 @@ + +
    +
    -
    -

    -How to benefit from compiled models

    +
    +

    How to benefit from compiled models +

    When using an mkin version equal to or greater than 0.9-36 and a C compiler is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. Starting from version 0.9.49.9, the mkinmod() function checks for presence of a compiler using

    -pkgbuild::has_compiler()
    -

    In previous versions, it used Sys.which("gcc") for this check.

    +pkgbuild::has_compiler()
    +

    In previous versions, it used Sys.which("gcc") for this check.

    On Linux, you need to have the essential build tools like make and gcc or clang installed. On Debian based linux distributions, these will be pulled in by installing the build-essential package.

    On MacOS, which I do not use personally, I have had reports that a compiler is available by default.

    On Windows, you need to install Rtools and have the path to its bin directory in your PATH variable. You do not need to modify the PATH variable when installing Rtools. Instead, I would recommend to put the line

    -Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))
    +Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))

    into your .Rprofile startup file. This is just a text file with some R code that is executed when your R session starts. It has to be named .Rprofile and has to be located in your home directory, which will generally be your Documents folder. You can check the location of the home directory used by R by issuing

    -Sys.getenv("HOME")
    +Sys.getenv("HOME")
    -
    -

    -Comparison with other solution methods

    +
    +

    Comparison with other solution methods +

    First, we build a simple degradation model for a parent compound with one metabolite, and we remove zero values from the dataset.

    -library("mkin", quietly = TRUE)
    -SFO_SFO <- mkinmod(
    -  parent = mkinsub("SFO", "m1"),
    -  m1 = mkinsub("SFO"))
    -
    ## Temporary DLL for differentials generated and loaded
    +library("mkin", quietly = TRUE) +SFO_SFO <- mkinmod( + parent = mkinsub("SFO", "m1"), + m1 = mkinsub("SFO"))
    +
    ## Temporary DLL for differentials generated and loaded
    -FOCUS_D <- subset(FOCUS_2006_D, value != 0)
    +FOCUS_D <- subset(FOCUS_2006_D, value != 0)

    We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed. Since mkin version 0.9.49.11, an analytical solution is also implemented, which is included in the tests below.

    -if (require(rbenchmark)) {
    -  b.1 <- benchmark(
    -    "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_D,
    -       solution_type = "deSolve",
    -       use_compiled = FALSE, quiet = TRUE),
    -    "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_D,
    -       solution_type = "eigen", quiet = TRUE),
    -    "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_D,
    -       solution_type = "deSolve", quiet = TRUE),
    -    "analytical" = mkinfit(SFO_SFO, FOCUS_D,
    -       solution_type = "analytical",
    -       use_compiled = FALSE, quiet = TRUE),
    -    replications = 1, order = "relative",
    -    columns = c("test", "replications", "relative", "elapsed"))
    -  print(b.1)
    -} else {
    -  print("R package rbenchmark is not available")
    -}
    -
    ##                    test replications relative elapsed
    -## 4            analytical            1    1.000   0.182
    -## 3     deSolve, compiled            1    1.824   0.332
    -## 2      Eigenvalue based            1    2.082   0.379
    -## 1 deSolve, not compiled            1   46.181   8.405
    +if (require(rbenchmark)) { + b.1 <- benchmark( + "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_D, + solution_type = "deSolve", + use_compiled = FALSE, quiet = TRUE), + "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_D, + solution_type = "eigen", quiet = TRUE), + "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_D, + solution_type = "deSolve", quiet = TRUE), + "analytical" = mkinfit(SFO_SFO, FOCUS_D, + solution_type = "analytical", + use_compiled = FALSE, quiet = TRUE), + replications = 1, order = "relative", + columns = c("test", "replications", "relative", "elapsed")) + print(b.1) +} else { + print("R package rbenchmark is not available") +}
    +
    ##                    test replications relative elapsed
    +## 4            analytical            1    1.000   0.186
    +## 3     deSolve, compiled            1    1.656   0.308
    +## 2      Eigenvalue based            1    2.102   0.391
    +## 1 deSolve, not compiled            1   38.968   7.248

    We see that using the compiled model is by more than a factor of 10 faster than using deSolve without compiled code.

    -
    -

    -Model without analytical solution

    +
    +

    Model without analytical solution +

    This evaluation is also taken from the example section of mkinfit. No analytical solution is available for this system, and now Eigenvalue based solution is possible, so only deSolve using with or without compiled code is available.

    -if (require(rbenchmark)) {
    -  FOMC_SFO <- mkinmod(
    -    parent = mkinsub("FOMC", "m1"),
    -    m1 = mkinsub( "SFO"))
    -
    -  b.2 <- benchmark(
    -    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_D,
    -                                      use_compiled = FALSE, quiet = TRUE),
    -    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE),
    -    replications = 1, order = "relative",
    -    columns = c("test", "replications", "relative", "elapsed"))
    -  print(b.2)
    -  factor_FOMC_SFO <- round(b.2["1", "relative"])
    -} else {
    -  factor_FOMC_SFO <- NA
    -  print("R package benchmark is not available")
    -}
    -
    ## Temporary DLL for differentials generated and loaded
    -
    ##                    test replications relative elapsed
    -## 2     deSolve, compiled            1    1.000   0.541
    -## 1 deSolve, not compiled            1   29.091  15.738
    +if (require(rbenchmark)) { + FOMC_SFO <- mkinmod( + parent = mkinsub("FOMC", "m1"), + m1 = mkinsub( "SFO")) + + b.2 <- benchmark( + "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_D, + use_compiled = FALSE, quiet = TRUE), + "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_D, quiet = TRUE), + replications = 1, order = "relative", + columns = c("test", "replications", "relative", "elapsed")) + print(b.2) + factor_FOMC_SFO <- round(b.2["1", "relative"]) +} else { + factor_FOMC_SFO <- NA + print("R package benchmark is not available") +}
    +
    ## Temporary DLL for differentials generated and loaded
    +
    ##                    test replications relative elapsed
    +## 2     deSolve, compiled            1    1.000   0.452
    +## 1 deSolve, not compiled            1   29.431  13.303

    Here we get a performance benefit of a factor of 29 using the version of the differential equation model compiled from C code!

    -

    This vignette was built with mkin 1.0.3.9000 on

    -
    ## R version 4.0.3 (2020-10-10)
    -## Platform: x86_64-pc-linux-gnu (64-bit)
    -## Running under: Debian GNU/Linux bullseye/sid
    -
    ## CPU model: AMD Ryzen 7 1700 Eight-Core Processor
    +

    This vignette was built with mkin 1.2.0 on

    +
    ## R version 4.2.2 (2022-10-31)
    +## Platform: x86_64-pc-linux-gnu (64-bit)
    +## Running under: Debian GNU/Linux 11 (bullseye)
    +
    ## CPU model: AMD Ryzen 7 1700 Eight-Core Processor
    @@ -211,11 +219,13 @@ @@ -224,5 +234,7 @@ + + diff --git a/docs/dev/articles/web_only/multistart.html b/docs/dev/articles/web_only/multistart.html index 0c08905a..50a57d1b 100644 --- a/docs/dev/articles/web_only/multistart.html +++ b/docs/dev/articles/web_only/multistart.html @@ -34,7 +34,7 @@ mkin - 1.1.2 + 1.2.0 @@ -109,7 +109,7 @@

    Short demo of the multistart method

    Johannes Ranke

    -

    Last change 26 September 2022 (rebuilt 2022-10-28)

    +

    Last change 26 September 2022 (rebuilt 2022-11-01)

    Source: vignettes/web_only/multistart.rmd @@ -144,23 +144,21 @@

    This confirms that the variance of k2 is the most problematic parameter, so we reduce the parameter distribution model by removing the intersoil variability for k2.

     f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2")
    -illparms(f_saem_reduced)
    -
    ## character(0)
    -
    -f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
    +illparms(f_saem_reduced)
    +f_saem_reduced_multi <- multistart(f_saem_reduced, n = 16, cores = 16)
     parplot(f_saem_reduced_multi, lpos = "topright")

    The results confirm that all remaining parameters can be determined with sufficient certainty.

    We can also analyse the log-likelihoods obtained in the multiple runs:

    -
    +
     llhist(f_saem_reduced_multi)

    The parameter histograms can be further improved by excluding the result with the low likelihood.

    -
    +
     parplot(f_saem_reduced_multi, lpos = "topright", llmin = -326, ylim = c(0.5, 2))

    We can use the anova method to compare the models, including a likelihood ratio test if the models are nested.

    -
    +
     anova(f_saem_full, best(f_saem_reduced_multi), test = TRUE)
    ## Data: 155 observations of 1 variable(s) grouped in 6 datasets
     ## 
    diff --git a/docs/dev/authors.html b/docs/dev/authors.html
    index 35ae54bd..bc48a6f1 100644
    --- a/docs/dev/authors.html
    +++ b/docs/dev/authors.html
    @@ -17,7 +17,7 @@
           
           
             mkin
    -        1.1.2
    +        1.2.0
           
         
    @@ -112,13 +112,13 @@

    Ranke J (2022). mkin: Kinetic Evaluation of Chemical Degradation Data. -R package version 1.1.2, https://pkgdown.jrwb.de/mkin/. +R package version 1.2.0, https://pkgdown.jrwb.de/mkin/.

    @Manual{,
       title = {mkin: Kinetic Evaluation of Chemical Degradation Data},
       author = {Johannes Ranke},
       year = {2022},
    -  note = {R package version 1.1.2},
    +  note = {R package version 1.2.0},
       url = {https://pkgdown.jrwb.de/mkin/},
     }
    diff --git a/docs/dev/index.html b/docs/dev/index.html index 5257b590..a64fb633 100644 --- a/docs/dev/index.html +++ b/docs/dev/index.html @@ -45,7 +45,7 @@ mkin - 1.1.2 + 1.2.0
    diff --git a/docs/dev/news/index.html b/docs/dev/news/index.html index b509aca3..1703be16 100644 --- a/docs/dev/news/index.html +++ b/docs/dev/news/index.html @@ -17,7 +17,7 @@ mkin - 1.1.2 + 1.2.0
    @@ -85,14 +85,15 @@
    - -
    • ‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with diagnostic plotting functions ‘llhist’ and ‘parplot’.

    • -
    • ‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.

    • -
    • ‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.

    • -
    • ‘R/saem.R’: ‘logLik’ and ‘update’ methods for ‘saem.mmkin’ objects.

    • -
    • ‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’ and ‘mhmkin’ objects.

    • + +
      • ‘R/mhmkin.R’: New method for performing multiple hierarchical mkin fits in one function call, optionally in parallel.

      • +
      • ‘R/mhmkin.R’: ‘anova.mhmkin’ for conveniently comparing the resulting fits.

      • ‘R/illparms.R’: New generic to show ill-defined parameters with methods for ‘mkinfit’, ‘mmkin’, ‘saem.mmkin’ and ‘mhmkin’ objects.

      • +
      • ‘R/multistart.R’: New method for testing multiple start parameters for hierarchical model fits, with function ‘llhist’ and new generic ‘parplot’ for diagnostics, and new generics ‘which.best’ and ‘best’ for extracting the fit with the highest likelihood

      • +
      • ‘R/saem.R’: ‘logLik’, ‘update’ and ‘anova’ methods for ‘saem.mmkin’ objects.

      • +
      • ‘R/status.R’: New generic to show status information for fit array objects with methods for ‘mmkin’, ‘mhmkin’ and ‘multistart’ objects.

      • ‘R/summary.mmkin.R’: Summary method for mmkin objects.

      • +
      • ‘R/saem.R’: Implement and test saemix transformations for FOMC and HS. Also, error out if saemix transformations are requested but not supported.

    diff --git a/docs/dev/pkgdown.yml b/docs/dev/pkgdown.yml index 12a9b003..aeea435d 100644 --- a/docs/dev/pkgdown.yml +++ b/docs/dev/pkgdown.yml @@ -12,7 +12,7 @@ articles: compiled_models: web_only/compiled_models.html dimethenamid_2018: web_only/dimethenamid_2018.html multistart: web_only/multistart.html -last_built: 2022-10-28T21:37Z +last_built: 2022-11-01T13:09Z urls: reference: https://pkgdown.jrwb.de/mkin/reference article: https://pkgdown.jrwb.de/mkin/articles diff --git a/docs/dev/reference/Rplot001.png b/docs/dev/reference/Rplot001.png index 6841f086..17a35806 100644 Binary files a/docs/dev/reference/Rplot001.png and b/docs/dev/reference/Rplot001.png differ diff --git a/docs/dev/reference/Rplot002.png b/docs/dev/reference/Rplot002.png index 11f6a1cd..f06a860e 100644 Binary files a/docs/dev/reference/Rplot002.png and b/docs/dev/reference/Rplot002.png differ diff --git a/docs/dev/reference/anova.saem.mmkin.html b/docs/dev/reference/anova.saem.mmkin.html index abe77c65..2c109cc2 100644 --- a/docs/dev/reference/anova.saem.mmkin.html +++ b/docs/dev/reference/anova.saem.mmkin.html @@ -1,6 +1,8 @@ -Anova method for saem.mmkin objects — anova.saem.mmkin • mkinAnova method for saem.mmkin objects — anova.saem.mmkin • mkin @@ -18,7 +20,7 @@ the saemix package. As in other prominent anova methods, models are sorted"> mkin - 1.1.2 + 1.2.0
    @@ -87,8 +89,10 @@ the saemix package. As in other prominent anova methods, models are sorted">
    -

    Generate an anova object. The method to calculate the BIC is that from -the saemix package. As in other prominent anova methods, models are sorted

    +

    Generate an anova object. The method to calculate the BIC is that from the +saemix package. As in other prominent anova methods, models are sorted by +number of parameters, and the tests (if requested) are always relative to +the model on the previous line.

    diff --git a/docs/dev/reference/aw.html b/docs/dev/reference/aw.html index 57dfa06c..e552cc62 100644 --- a/docs/dev/reference/aw.html +++ b/docs/dev/reference/aw.html @@ -19,7 +19,7 @@ by Burnham and Anderson (2004)."> mkin - 1.1.2 + 1.2.0
    @@ -52,11 +52,14 @@ likelihood function.">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
  • @@ -378,17 +381,17 @@ Degradation Data. Environments 6(12) 124 # Use shorthand notation for parent only degradation fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit) -#> mkin version used for fitting: 1.1.2 -#> R version used for fitting: 4.2.1 -#> Date of fit: Fri Sep 16 10:29:10 2022 -#> Date of summary: Fri Sep 16 10:29:10 2022 +#> mkin version used for fitting: 1.2.0 +#> R version used for fitting: 4.2.2 +#> Date of fit: Tue Nov 1 14:09:26 2022 +#> Date of summary: Tue Nov 1 14:09:26 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent #> #> Model predictions using solution type analytical #> -#> Fitted using 222 model solutions performed in 0.045 s +#> Fitted using 222 model solutions performed in 0.049 s #> #> Error model: Constant variance #> @@ -530,9 +533,9 @@ Degradation Data. Environments 6(12) 124 } #> Loading required package: rbenchmark #> test relative elapsed -#> 3 analytical 1.000 0.577 -#> 1 deSolve_compiled 1.537 0.887 -#> 2 eigen 2.551 1.472 +#> 3 analytical 1.000 0.559 +#> 1 deSolve_compiled 1.556 0.870 +#> 2 eigen 2.603 1.455 # } # Use stepwise fitting, using optimised parameters from parent only fit, FOMC-SFO @@ -559,10 +562,10 @@ Degradation Data. Environments 6(12) 124 #> Warning: NaNs produced #> Warning: NaNs produced #> Warning: diag(.) had 0 or NA entries; non-finite result is doubtful -#> mkin version used for fitting: 1.1.2 -#> R version used for fitting: 4.2.1 -#> Date of fit: Fri Sep 16 10:29:21 2022 -#> Date of summary: Fri Sep 16 10:29:21 2022 +#> mkin version used for fitting: 1.2.0 +#> R version used for fitting: 4.2.2 +#> Date of fit: Tue Nov 1 14:09:37 2022 +#> Date of summary: Tue Nov 1 14:09:37 2022 #> #> Equations: #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -571,7 +574,7 @@ Degradation Data. Environments 6(12) 124 #> #> Model predictions using solution type deSolve #> -#> Fitted using 3729 model solutions performed in 2.48 s +#> Fitted using 3729 model solutions performed in 2.43 s #> #> Error model: Two-component variance function #> diff --git a/docs/dev/reference/multistart.html b/docs/dev/reference/multistart.html index 176d40c0..3f5c4b35 100644 --- a/docs/dev/reference/multistart.html +++ b/docs/dev/reference/multistart.html @@ -22,7 +22,7 @@ mixed-effects models by Duchesne et al (2021)."> mkin - 1.1.2 + 1.2.0 @@ -202,7 +202,6 @@ doi: 10.1186/s12859-021-04373-4.

    f_saem_reduced <- update(f_saem_full, no_random_effect = "log_k2") illparms(f_saem_reduced) -#> character(0) # On Windows, we need to create a cluster first. When working with # such a cluster, we need to export the mmkin object to the cluster # nodes, as it is referred to when updating the saem object on the nodes. diff --git a/docs/dev/reference/parms.html b/docs/dev/reference/parms.html index 949bb2f9..95db0593 100644 --- a/docs/dev/reference/parms.html +++ b/docs/dev/reference/parms.html @@ -19,7 +19,7 @@ without considering the error structure that was assumed for the fit."> mkin - 1.1.2 + 1.2.0 diff --git a/docs/dev/reference/parplot.html b/docs/dev/reference/parplot.html index 38a93e27..ffe93e6c 100644 --- a/docs/dev/reference/parplot.html +++ b/docs/dev/reference/parplot.html @@ -19,7 +19,7 @@ or by their medians as proposed in the paper by Duchesne et al. (2021)."> mkin - 1.1.2 + 1.2.0 diff --git a/docs/dev/reference/plot.mixed.mmkin-4.png b/docs/dev/reference/plot.mixed.mmkin-4.png index d2fa1ae1..a849aaee 100644 Binary files a/docs/dev/reference/plot.mixed.mmkin-4.png and b/docs/dev/reference/plot.mixed.mmkin-4.png differ diff --git a/docs/dev/reference/plot.mixed.mmkin.html b/docs/dev/reference/plot.mixed.mmkin.html index 83017908..b1c62721 100644 --- a/docs/dev/reference/plot.mixed.mmkin.html +++ b/docs/dev/reference/plot.mixed.mmkin.html @@ -17,7 +17,7 @@ mkin - 1.1.2 + 1.2.0 @@ -44,11 +44,14 @@ 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
  • @@ -96,6 +99,7 @@ xlab = "Time", xlim = range(x$data$time), resplot = c("predicted", "time"), + pop_curve = "auto", pred_over = NULL, test_log_parms = FALSE, conf.level = 0.6, @@ -149,6 +153,12 @@ variables in the model.

    predicted values?

    +
    pop_curve
    +

    Per default, a population curve is drawn in case +population parameters are fitted by the model, e.g. for saem objects. +In case there is a covariate model, no population curve is currently shown.

    + +
    pred_over

    Named list of alternative predictions as obtained from mkinpredict with a compatible mkinmod.

    diff --git a/docs/dev/reference/saem.html b/docs/dev/reference/saem.html index c8a7504f..8ea0ef6e 100644 --- a/docs/dev/reference/saem.html +++ b/docs/dev/reference/saem.html @@ -19,7 +19,7 @@ Expectation Maximisation algorithm (SAEM)."> mkin - 1.1.2 + 1.2.0 @@ -100,6 +100,7 @@ Expectation Maximisation algorithm (SAEM).

    saem( object, transformations = c("mkin", "saemix"), + error_model = "auto", degparms_start = numeric(), test_log_parms = TRUE, conf.level = 0.6, @@ -124,6 +125,7 @@ Expectation Maximisation algorithm (SAEM).

    object, solution_type = "auto", transformations = c("mkin", "saemix"), + error_model = "auto", degparms_start = numeric(), covariance.model = "auto", no_random_effect = NULL, @@ -160,6 +162,10 @@ SFO, FOMC, DFOP and HS without fixing parent_0, and SFO or DFOP wit one SFO metabolite.

    +
    error_model
    +

    Possibility to override the error model used in the mmkin object

    + +
    degparms_start

    Parameter values given as a named numeric vector will be used to override the starting values obtained from the 'mmkin' object.

    @@ -409,10 +415,10 @@ using mmkin.

    summary(f_saem_dfop_sfo, data = TRUE) #> saemix version used for fitting: 3.2 -#> mkin version used for pre-fitting: 1.1.2 -#> R version used for fitting: 4.2.1 -#> Date of fit: Wed Oct 26 09:20:37 2022 -#> Date of summary: Wed Oct 26 09:20:37 2022 +#> mkin version used for pre-fitting: 1.2.0 +#> R version used for fitting: 4.2.2 +#> Date of fit: Tue Nov 1 14:12:07 2022 +#> Date of summary: Tue Nov 1 14:12:07 2022 #> #> Equations: #> d_parent/dt = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 * @@ -427,7 +433,7 @@ using mmkin.

    #> #> Model predictions using solution type analytical #> -#> Fitted in 8.902 s +#> Fitted in 8.45 s #> Using 300, 100 iterations and 10 chains #> #> Variance model: Constant variance diff --git a/docs/dev/reference/set_nd_nq.html b/docs/dev/reference/set_nd_nq.html index 26a28339..6c6a5d46 100644 --- a/docs/dev/reference/set_nd_nq.html +++ b/docs/dev/reference/set_nd_nq.html @@ -21,7 +21,7 @@ it automates the proposal of Boesten et al (2015)."> mkin - 1.1.2 + 1.2.0 diff --git a/docs/dev/reference/status.html b/docs/dev/reference/status.html index 778446b3..4c856100 100644 --- a/docs/dev/reference/status.html +++ b/docs/dev/reference/status.html @@ -17,7 +17,7 @@ mkin - 1.1.2 + 1.2.0 diff --git a/docs/dev/reference/summary.mkinfit.html b/docs/dev/reference/summary.mkinfit.html index c58fffbb..993544c7 100644 --- a/docs/dev/reference/summary.mkinfit.html +++ b/docs/dev/reference/summary.mkinfit.html @@ -21,7 +21,7 @@ values.">