From ef7ccf68e086bac3e75858bd4b97e3a2c6872aa1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Jun 2016 00:44:48 +0200 Subject: Avoid multicore fits in vignettes for passing CRAN checks Also a small fix to the FOCUS Z vignette, and an update of the static documentation generated by staticdocs. --- DESCRIPTION | 2 +- build.log | 2 +- inst/web/DFOP.solution.html | 4 +- inst/web/Extract.mmkin.html | 28 +- inst/web/FOCUS_2006_DFOP_ref_A_to_B.html | 4 +- inst/web/FOCUS_2006_FOMC_ref_A_to_F.html | 4 +- inst/web/FOCUS_2006_HS_ref_A_to_F.html | 4 +- inst/web/FOCUS_2006_SFO_ref_A_to_F.html | 4 +- inst/web/FOCUS_2006_datasets.html | 4 +- inst/web/FOMC.solution.html | 4 +- inst/web/HS.solution.html | 4 +- inst/web/IORE.solution.html | 4 +- inst/web/SFO.solution.html | 4 +- inst/web/SFORB.solution.html | 4 +- inst/web/add_err-4.png | Bin 0 -> 26529 bytes inst/web/add_err-6.png | Bin 0 -> 15790 bytes inst/web/add_err-8.png | Bin 0 -> 14745 bytes inst/web/add_err.html | 200 ++++++++++ inst/web/endpoints.html | 4 +- inst/web/geometric_mean.html | 4 +- inst/web/ilr.html | 4 +- inst/web/index.html | 20 +- inst/web/mccall81_245T.html | 14 +- inst/web/mkin_long_to_wide.html | 4 +- inst/web/mkin_wide_to_long.html | 4 +- inst/web/mkinds.html | 4 +- inst/web/mkinerrmin.html | 4 +- inst/web/mkinfit.html | 27 +- inst/web/mkinmod.html | 4 +- inst/web/mkinparplot.html | 4 +- inst/web/mkinplot.html | 4 +- inst/web/mkinpredict.html | 12 +- inst/web/mkinresplot.html | 4 +- inst/web/mkinsub.html | 4 +- inst/web/mmkin.html | 30 +- inst/web/plot.mkinfit-10.png | Bin 0 -> 18223 bytes inst/web/plot.mkinfit-6.png | Bin 0 -> 16820 bytes inst/web/plot.mkinfit-8.png | Bin 0 -> 13696 bytes inst/web/plot.mkinfit.html | 82 +++- inst/web/plot.mmkin-6.png | Bin 0 -> 7916 bytes inst/web/plot.mmkin.html | 23 +- inst/web/print.mkinds.html | 4 +- inst/web/print.mkinmod.html | 4 +- inst/web/schaefer07_complex_case.html | 4 +- inst/web/summary.mkinfit.html | 14 +- inst/web/synthetic_data_for_UBA.html | 4 +- inst/web/transform_odeparms.html | 14 +- inst/web/vignettes/FOCUS_D.html | 89 ++++- inst/web/vignettes/FOCUS_L.html | 644 +++++++++++++++---------------- inst/web/vignettes/FOCUS_Z.pdf | Bin 225057 -> 237947 bytes inst/web/vignettes/compiled_models.html | 230 +++++++++-- inst/web/vignettes/mkin.html | 347 +++++++++++++++++ vignettes/FOCUS_D.html | 89 ++++- vignettes/FOCUS_L.Rmd | 6 +- vignettes/FOCUS_L.html | 66 ++-- vignettes/FOCUS_Z.Rnw | 2 +- vignettes/FOCUS_Z.pdf | Bin 225057 -> 237947 bytes vignettes/compiled_models.html | 230 +++++++++-- vignettes/mkin.html | 7 +- 59 files changed, 1636 insertions(+), 650 deletions(-) create mode 100644 inst/web/add_err-4.png create mode 100644 inst/web/add_err-6.png create mode 100644 inst/web/add_err-8.png create mode 100644 inst/web/add_err.html create mode 100644 inst/web/plot.mkinfit-10.png create mode 100644 inst/web/plot.mkinfit-6.png create mode 100644 inst/web/plot.mkinfit-8.png create mode 100644 inst/web/plot.mmkin-6.png create mode 100644 inst/web/vignettes/mkin.html diff --git a/DESCRIPTION b/DESCRIPTION index 76b686c5..257e53cb 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: mkin Type: Package -Title: Kinetic evaluation of chemical degradation data +Title: Kinetic Evaluation of Chemical Degradation Data Version: 0.9.43 Date: 2016-06-28 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), diff --git a/build.log b/build.log index c497bbbe..a8446671 100644 --- a/build.log +++ b/build.log @@ -6,5 +6,5 @@ * checking for LF line-endings in source and make files * checking for empty or unneeded directories * looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.42.9000.tar.gz’ +* building ‘mkin_0.9.44.tar.gz’ diff --git a/inst/web/DFOP.solution.html b/inst/web/DFOP.solution.html index fb73ffb8..4746beef 100644 --- a/inst/web/DFOP.solution.html +++ b/inst/web/DFOP.solution.html @@ -2,7 +2,7 @@ -DFOP.solution. mkin 0.9.42 +DFOP.solution. mkin 0.9.43 @@ -32,7 +32,7 @@
- mkin 0.9.42 + mkin 0.9.43
  • Index
    • diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index f31692de..60697959 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -2,7 +2,7 @@ -[.mmkin. mkin 0.9.42 +[.mmkin. mkin 0.9.43
    - mkin 0.9.42 + mkin 0.9.43
    • Index
      • @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.284 0.000 0.286 + 0.704 0.000 0.702 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x1bdcb08> +<environment: 0x49ead78> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x1bdcb08> +<environment: 0x49ead78> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Thu Mar 24 08:28:51 2016" +[1] "Tue Jun 28 01:17:01 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.088 0.008 0.096 + 0.208 0.004 0.208 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x3827398> +<environment: 0x5a6c3b0> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x3827398> +<environment: 0x5a6c3b0> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Thu Mar 24 08:28:51 2016" +[1] "Tue Jun 28 01:17:00 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.088 0.008 0.096 + 0.208 0.004 0.208 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x3827398> +<environment: 0x5a6c3b0> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x3827398> +<environment: 0x5a6c3b0> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Thu Mar 24 08:28:51 2016" +[1] "Tue Jun 28 01:17:00 2016" attr(,"class") [1] "mkinfit" "modFit" diff --git a/inst/web/FOCUS_2006_DFOP_ref_A_to_B.html b/inst/web/FOCUS_2006_DFOP_ref_A_to_B.html index 76911ba7..e5dad993 100644 --- a/inst/web/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/inst/web/FOCUS_2006_DFOP_ref_A_to_B.html @@ -2,7 +2,7 @@ -FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.42 +FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.43 @@ -32,7 +32,7 @@
      - mkin 0.9.42 + mkin 0.9.43
      • Index
        • diff --git a/inst/web/FOCUS_2006_FOMC_ref_A_to_F.html b/inst/web/FOCUS_2006_FOMC_ref_A_to_F.html index ac250110..ce238c92 100644 --- a/inst/web/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/inst/web/FOCUS_2006_FOMC_ref_A_to_F.html @@ -2,7 +2,7 @@ -FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.42 +FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.43 @@ -32,7 +32,7 @@
        - mkin 0.9.42 + mkin 0.9.43
        • Index
          • diff --git a/inst/web/FOCUS_2006_HS_ref_A_to_F.html b/inst/web/FOCUS_2006_HS_ref_A_to_F.html index e7f5cdd5..a1abc1b6 100644 --- a/inst/web/FOCUS_2006_HS_ref_A_to_F.html +++ b/inst/web/FOCUS_2006_HS_ref_A_to_F.html @@ -2,7 +2,7 @@ -FOCUS_2006_HS_ref_A_to_F. mkin 0.9.42 +FOCUS_2006_HS_ref_A_to_F. mkin 0.9.43 @@ -32,7 +32,7 @@
          - mkin 0.9.42 + mkin 0.9.43
          • Index
            • diff --git a/inst/web/FOCUS_2006_SFO_ref_A_to_F.html b/inst/web/FOCUS_2006_SFO_ref_A_to_F.html index 5bbdaa24..badb4c41 100644 --- a/inst/web/FOCUS_2006_SFO_ref_A_to_F.html +++ b/inst/web/FOCUS_2006_SFO_ref_A_to_F.html @@ -2,7 +2,7 @@ -FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.42 +FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.43 @@ -32,7 +32,7 @@
            - mkin 0.9.42 + mkin 0.9.43
            • Index
              • diff --git a/inst/web/FOCUS_2006_datasets.html b/inst/web/FOCUS_2006_datasets.html index a2ea626c..7aa7f78b 100644 --- a/inst/web/FOCUS_2006_datasets.html +++ b/inst/web/FOCUS_2006_datasets.html @@ -2,7 +2,7 @@ -FOCUS_2006_datasets. mkin 0.9.42 +FOCUS_2006_datasets. mkin 0.9.43 @@ -32,7 +32,7 @@
              - mkin 0.9.42 + mkin 0.9.43
              • Index
                • diff --git a/inst/web/FOMC.solution.html b/inst/web/FOMC.solution.html index 2f6a4097..5c17afe4 100644 --- a/inst/web/FOMC.solution.html +++ b/inst/web/FOMC.solution.html @@ -2,7 +2,7 @@ -FOMC.solution. mkin 0.9.42 +FOMC.solution. mkin 0.9.43 @@ -32,7 +32,7 @@
                - mkin 0.9.42 + mkin 0.9.43
                • Index
                  • diff --git a/inst/web/HS.solution.html b/inst/web/HS.solution.html index d009aa98..7f84cccd 100644 --- a/inst/web/HS.solution.html +++ b/inst/web/HS.solution.html @@ -2,7 +2,7 @@ -HS.solution. mkin 0.9.42 +HS.solution. mkin 0.9.43 @@ -32,7 +32,7 @@
                  - mkin 0.9.42 + mkin 0.9.43
                  • Index
                    • diff --git a/inst/web/IORE.solution.html b/inst/web/IORE.solution.html index 1491bccb..f735b3ad 100644 --- a/inst/web/IORE.solution.html +++ b/inst/web/IORE.solution.html @@ -2,7 +2,7 @@ -IORE.solution. mkin 0.9.42 +IORE.solution. mkin 0.9.43 @@ -32,7 +32,7 @@
                    - mkin 0.9.42 + mkin 0.9.43
                    • Index
                      • diff --git a/inst/web/SFO.solution.html b/inst/web/SFO.solution.html index 33ba8778..2f0d2ff1 100644 --- a/inst/web/SFO.solution.html +++ b/inst/web/SFO.solution.html @@ -2,7 +2,7 @@ -SFO.solution. mkin 0.9.42 +SFO.solution. mkin 0.9.43 @@ -32,7 +32,7 @@
                      - mkin 0.9.42 + mkin 0.9.43
                      • Index
                        • diff --git a/inst/web/SFORB.solution.html b/inst/web/SFORB.solution.html index 42c5a57f..0285188b 100644 --- a/inst/web/SFORB.solution.html +++ b/inst/web/SFORB.solution.html @@ -2,7 +2,7 @@ -SFORB.solution. mkin 0.9.42 +SFORB.solution. mkin 0.9.43 @@ -32,7 +32,7 @@
                        - mkin 0.9.42 + mkin 0.9.43
                        • Index
                          • diff --git a/inst/web/add_err-4.png b/inst/web/add_err-4.png new file mode 100644 index 00000000..af715972 Binary files /dev/null and b/inst/web/add_err-4.png differ diff --git a/inst/web/add_err-6.png b/inst/web/add_err-6.png new file mode 100644 index 00000000..1437d348 Binary files /dev/null and b/inst/web/add_err-6.png differ diff --git a/inst/web/add_err-8.png b/inst/web/add_err-8.png new file mode 100644 index 00000000..bc511434 Binary files /dev/null and b/inst/web/add_err-8.png differ diff --git a/inst/web/add_err.html b/inst/web/add_err.html new file mode 100644 index 00000000..67ff8f70 --- /dev/null +++ b/inst/web/add_err.html @@ -0,0 +1,200 @@ + + + + +add_err. mkin 0.9.43 + + + + + + + + + + + + + + + +
                          +
                          +
                          + mkin 0.9.43 +
                          + +
                          +
                          +
                          +
                          + +
                          +
                          + +
                          + +

                          + Add normally distributed errors to simulated kinetic degradation data +

                          + +
                          +
                          +

                          Usage

                          + 
                          add_err(prediction, sdfunc, n = 1000, LOD = 0.1, reps = 2,  digits = 1, seed = NA)
                          + +

                          Arguments

                          +
                          +
                          prediction
                          +
                          + A prediction from a kinetic model as produced by mkinpredict. +
                          +
                          sdfunc
                          +
                          + A function taking the predicted value as its only argument and returning + a standard deviation that should be used for generating the random error + terms for this value. +
                          +
                          n
                          +
                          + The number of datasets to be generated. +
                          +
                          LOD
                          +
                          + The limit of detection (LOD). Values that are below the LOD after adding + the random error will be set to NA. +
                          +
                          reps
                          +
                          + The number of replicates to be generated within the datasets. +
                          +
                          digits
                          +
                          + The number of digits to which the values will be rounded. +
                          +
                          seed
                          +
                          + The seed used for the generation of random numbers. If NA, the seed + is not set. +
                          +
                          + +
                          +

                          Description

                          + +

                          Normally distributed errors are added to data predicted for a specific + degradation model using mkinpredict. The variance of the error + may depend on the predicted value and is specified as a standard deviation.

                          + +
                          + +
                          +

                          Value

                          + +

                          + A list of datasets compatible with mmkin, i.e. + the components of the list are datasets compatible with + mkinfit. +

                          + +
                          + +
                          +

                          References

                          + +

                          Ranke J and Lehmann R (2015) To t-test or not to t-test, that is the question. XV Symposium on Pesticide Chemistry 2-4 September 2015, Piacenza, Italy + http://chem.uft.uni-bremen.de/ranke/posters/piacenza_2015.pdf

                          + +
                          + +

                          Examples

                          + 
                          # The kinetic model
+m_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
+                     M1 = mkinsub("SFO"), use_of_ff = "max")
+
                          
+Successfully compiled differential equation model from auto-generated C code.
+
                          
+# Generate a prediction for a specific set of parameters
+sampling_times = c(0, 1, 3, 7, 14, 28, 60, 90, 120)
+
+# This is the prediction used for the "Type 2 datasets" on the Piacenza poster
+# from 2015
+d_SFO_SFO <- mkinpredict(m_SFO_SFO,
+                         c(k_parent = 0.1, f_parent_to_M1 = 0.5,
+                           k_M1 = log(2)/1000),
+                         c(parent = 100, M1 = 0),
+                         sampling_times)
+
+# Add an error term with a constant (independent of the value) standard deviation
+# of 10, and generate three datasets
+d_SFO_SFO_err <- add_err(d_SFO_SFO, function(x) 10, n = 3, seed = 123456789 )
+
+# Name the datasets for nicer plotting
+names(d_SFO_SFO_err) <- paste("Dataset", 1:3)
+
+# Name the model in the list of models (with only one member in this case)
+# for nicer plotting later on.
+# Be quiet and use the faster Levenberg-Marquardt algorithm, as the datasets
+# are easy and examples are run often. Use only one core not to offend CRAN
+# checks
+f_SFO_SFO <- mmkin(list("SFO-SFO" = m_SFO_SFO), 
+                   d_SFO_SFO_err, cores = 1,
+                   quiet = TRUE, method.modFit = "Marq")
+
+plot(f_SFO_SFO)
+
                          
+
                          
+
                          
+# We would like to inspect the fit for dataset 3 more closely
+# Using double brackets makes the returned object an mkinfit object
+# instead of a list of mkinfit objects, so plot.mkinfit is used
+plot(f_SFO_SFO[[3]], show_residuals = TRUE)
+
                          
+
                          
+
                          
+# If we use single brackets, we should give two indices (model and dataset),
+# and plot.mmkin is used
+plot(f_SFO_SFO[1, 3])
+
                          
+
                          
+
                          +
                          +
                          + + + +

                          Author

                          + + Johannes Ranke + + +
                          +
                          + + +
                          + + \ No newline at end of file diff --git a/inst/web/endpoints.html b/inst/web/endpoints.html index 9ddcc8b4..0566d93f 100644 --- a/inst/web/endpoints.html +++ b/inst/web/endpoints.html @@ -2,7 +2,7 @@ -endpoints. mkin 0.9.42 +endpoints. mkin 0.9.43
                          - mkin 0.9.42 + mkin 0.9.43
                          • Index
                            • diff --git a/inst/web/geometric_mean.html b/inst/web/geometric_mean.html index 9d47ebdc..82caad0e 100644 --- a/inst/web/geometric_mean.html +++ b/inst/web/geometric_mean.html @@ -2,7 +2,7 @@ -geometric_mean. mkin 0.9.42 +geometric_mean. mkin 0.9.43 @@ -32,7 +32,7 @@
                            - mkin 0.9.42 + mkin 0.9.43
                            • Index
                              • diff --git a/inst/web/ilr.html b/inst/web/ilr.html index cb0eef23..bcf1fc26 100644 --- a/inst/web/ilr.html +++ b/inst/web/ilr.html @@ -2,7 +2,7 @@ -ilr. mkin 0.9.42 +ilr. mkin 0.9.43
                              - mkin 0.9.42 + mkin 0.9.43

                              Dependencies

                              diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 6266c0b5..6596bd70 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -2,7 +2,7 @@ -mccall81_245T. mkin 0.9.42 +mccall81_245T. mkin 0.9.43 @@ -32,7 +32,7 @@
                              - mkin 0.9.42 + mkin 0.9.43
                              • Index
                                • @@ -112,10 +112,10 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
                              -
                              mkin version: 0.9.42 -R version: 3.2.4 -Date of fit: Thu Mar 24 08:28:59 2016 -Date of summary: Thu Mar 24 08:28:59 2016 +
                              mkin version: 0.9.43 +R version: 3.3.1 +Date of fit: Tue Jun 28 01:17:19 2016 +Date of summary: Tue Jun 28 01:17:19 2016 Equations: d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -124,7 +124,7 @@ d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole Model predictions using solution type deSolve -Fitted with method Port using 246 model solutions performed in 1.454 s +Fitted with method Port using 246 model solutions performed in 3.778 s Weighting: none diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index de36532f..e58ce305 100644 --- a/inst/web/mkin_long_to_wide.html +++ b/inst/web/mkin_long_to_wide.html @@ -2,7 +2,7 @@ -mkin_long_to_wide. mkin 0.9.42 +mkin_long_to_wide. mkin 0.9.43
                              - mkin 0.9.42 + mkin 0.9.43
                              • Index
                                • diff --git a/inst/web/mkin_wide_to_long.html b/inst/web/mkin_wide_to_long.html index 08abc942..ab4f7dbb 100644 --- a/inst/web/mkin_wide_to_long.html +++ b/inst/web/mkin_wide_to_long.html @@ -2,7 +2,7 @@ -mkin_wide_to_long. mkin 0.9.42 +mkin_wide_to_long. mkin 0.9.43
                                - mkin 0.9.42 + mkin 0.9.43
                                • Index
                                  • diff --git a/inst/web/mkinds.html b/inst/web/mkinds.html index 5e0f5001..f89128bf 100644 --- a/inst/web/mkinds.html +++ b/inst/web/mkinds.html @@ -2,7 +2,7 @@ -mkinds. mkin 0.9.42 +mkinds. mkin 0.9.43 @@ -32,7 +32,7 @@
                                  - mkin 0.9.42 + mkin 0.9.43
                                  • Index
                                    • diff --git a/inst/web/mkinerrmin.html b/inst/web/mkinerrmin.html index f5ab043f..ba665376 100644 --- a/inst/web/mkinerrmin.html +++ b/inst/web/mkinerrmin.html @@ -2,7 +2,7 @@ -mkinerrmin. mkin 0.9.42 +mkinerrmin. mkin 0.9.43 @@ -32,7 +32,7 @@
                                    - mkin 0.9.42 + mkin 0.9.43
                                    • Index
                                      • diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 07987fc2..dd7f1831 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -2,7 +2,7 @@ -mkinfit. mkin 0.9.42 +mkinfit. mkin 0.9.43
                                      - mkin 0.9.42 + mkin 0.9.43
                                      • Index
                                        • @@ -75,9 +75,9 @@ name of the observed variable for each data point. The second column must contain the times of observation, named "time". The third column must be named "value" and contain the observed values. Optionally, a further column - can contain weights for each data point. If it is not named "err", its name - must be passed as a further argument named err which is then passed - on to modFit. + can contain weights for each data point. Its name must be passed as a + further argument named err which is then passed on to + modFit.
                                        parms.ini
                                        @@ -323,17 +323,17 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
                                      -
                                      mkin version: 0.9.42 -R version: 3.2.4 -Date of fit: Thu Mar 24 08:29:01 2016 -Date of summary: Thu Mar 24 08:29:01 2016 +
                                      mkin version: 0.9.43 +R version: 3.3.1 +Date of fit: Tue Jun 28 01:17:26 2016 +Date of summary: Tue Jun 28 01:17:26 2016 Equations: d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent Model predictions using solution type analytical -Fitted with method Port using 64 model solutions performed in 0.195 s +Fitted with method Port using 64 model solutions performed in 0.457 s Weighting: none @@ -409,7 +409,7 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
                                      user system elapsed - 1.276 1.196 0.935 + 2.868 2.284 2.301
                                      coef(fit)
                                      @@ -473,9 +473,8 @@ m1 131.760712 437.69961 # summary(f.irls) # f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean") # summary(f.w.mean) -# f.w.mean.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", -# reweight.method = "obs") -# summary(f.w.mean.irls) +# f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value") +# summary(f.w.value) # ## End(Not run) ## Not run: diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index b3a396b9..0a361956 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9.42 +mkinmod. mkin 0.9.43
                                      - mkin 0.9.42 + mkin 0.9.43
                                      • Index
                                        • diff --git a/inst/web/mkinparplot.html b/inst/web/mkinparplot.html index 8eee6868..59fddb39 100644 --- a/inst/web/mkinparplot.html +++ b/inst/web/mkinparplot.html @@ -2,7 +2,7 @@ -mkinparplot. mkin 0.9.42 +mkinparplot. mkin 0.9.43
                                        - mkin 0.9.42 + mkin 0.9.43
                                        • Index
                                          • diff --git a/inst/web/mkinplot.html b/inst/web/mkinplot.html index c4542072..1b9a8a02 100644 --- a/inst/web/mkinplot.html +++ b/inst/web/mkinplot.html @@ -2,7 +2,7 @@ -mkinplot. mkin 0.9.42 +mkinplot. mkin 0.9.43
                                          - mkin 0.9.42 + mkin 0.9.43
                                          • Index
                                            • diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index 94c7a011..d64a075f 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -2,7 +2,7 @@ -mkinpredict. mkin 0.9.42 +mkinpredict. mkin 0.9.43
                                            - mkin 0.9.42 + mkin 0.9.43
                                            • Index
                                              • @@ -50,7 +50,7 @@

                                              - Produce predictions from a kinetic model using specifc parameters + Produce predictions from a kinetic model using specific parameters

                                              @@ -304,7 +304,7 @@ 201 20 4.978707 27.46227
                                              user system elapsed - 0.008 0.020 0.004 + 0.024 0.048 0.010
                                              system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -315,7 +315,7 @@ 201 20 4.978707 27.46227
                                              user system elapsed - 0.000 0.024 0.003 + 0.008 0.020 0.005
                                              system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -326,7 +326,7 @@ 201 20 4.978707 27.46227
                                              user system elapsed - 0.052 0.000 0.052 + 0.132 0.004 0.138
                                            diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index 5a2388dc..b5f32633 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9.42 +mkinresplot. mkin 0.9.43
                                            - mkin 0.9.42 + mkin 0.9.43
                                            • Index
                                              • diff --git a/inst/web/mkinsub.html b/inst/web/mkinsub.html index 2b92fbbc..bd8e1de6 100644 --- a/inst/web/mkinsub.html +++ b/inst/web/mkinsub.html @@ -2,7 +2,7 @@ -mkinsub. mkin 0.9.42 +mkinsub. mkin 0.9.43
                                              - mkin 0.9.42 + mkin 0.9.43
                                              • Index
                                                • diff --git a/inst/web/mmkin.html b/inst/web/mmkin.html index 754be268..b3e7a6fd 100644 --- a/inst/web/mmkin.html +++ b/inst/web/mmkin.html @@ -2,7 +2,7 @@ -mmkin. mkin 0.9.42 +mmkin. mkin 0.9.43
                                                - mkin 0.9.42 + mkin 0.9.43
                                                • Index
                                                  • @@ -107,24 +107,36 @@

                                                  Examples

                                                  ## Not run: 
-# 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")
+# m_synth_SFO_lin <- mkinmod(parent = mkinsub("SFO", "M1"),
+#                            M1 = mkinsub("SFO", "M2"),
+#                            M2 = mkinsub("SFO"), use_of_ff = "max")
 # 
-# m_synth_FOMC_lin <- mkinmod(parent = list(type = "FOMC", to = "M1"),
-#                            M1 = list(type = "SFO", to = "M2"),
-#                            M2 = list(type = "SFO"), use_of_ff = "max")
+# m_synth_FOMC_lin <- mkinmod(parent = mkinsub("FOMC", "M1"),
+#                             M1 = mkinsub("SFO", "M2"),
+#                             M2 = mkinsub("SFO"), use_of_ff = "max")
 # 
 # models <- list(SFO_lin = m_synth_SFO_lin, FOMC_lin = m_synth_FOMC_lin)
 # datasets <- lapply(synthetic_data_for_UBA_2014[1:3], function(x) x$data)
+# names(datasets) <- paste("Dataset", 1:3)
 # 
-# time_default <- system.time(fits <- mmkin(models, datasets))
+# time_default <- system.time(fits.0 <- mmkin(models, datasets))
 # time_1 <- system.time(fits.1 <- mmkin(models, datasets, cores = 1))
 # 
 # time_default
 # time_1
 # 
 # endpoints(fits[["SFO_lin", 2]])
+# 
+# # Plot.mkinfit handles rows or columns of mmkin result objects
+# plot(fits.0[1, ])
+# plot(fits.0[1, ], obs_var = c("M1", "M2"))
+# plot(fits.0[, 1])
+# # Use double brackets to extract a single mkinfit object, which will be plotted
+# # by plot.mkinfit
+# plot(fits.0[[1, 1]], sep_obs = TRUE, show_residuals = TRUE, show_errmin = TRUE)
+# # Plotting with mmkin (single brackets, extracting an mmkin object) does not
+# # allow to plot the observed variables separately
+# plot(fits.0[1, 1])
 # ## End(Not run)
                                                diff --git a/inst/web/plot.mkinfit-10.png b/inst/web/plot.mkinfit-10.png new file mode 100644 index 00000000..e657ab43 Binary files /dev/null and b/inst/web/plot.mkinfit-10.png differ diff --git a/inst/web/plot.mkinfit-6.png b/inst/web/plot.mkinfit-6.png new file mode 100644 index 00000000..ae10992b Binary files /dev/null and b/inst/web/plot.mkinfit-6.png differ diff --git a/inst/web/plot.mkinfit-8.png b/inst/web/plot.mkinfit-8.png new file mode 100644 index 00000000..24c5d9c4 Binary files /dev/null and b/inst/web/plot.mkinfit-8.png differ diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html index 1da0c8e8..9642b345 100644 --- a/inst/web/plot.mkinfit.html +++ b/inst/web/plot.mkinfit.html @@ -2,7 +2,7 @@ -plot.mkinfit. mkin 0.9.42 +plot.mkinfit. mkin 0.9.43
                                                - mkin 0.9.42 + mkin 0.9.43
                                                • Index
                                                  • @@ -56,7 +56,8 @@

                                                  Usage

                                                  - 
                                                  "plot"(x, fit = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", ylab = "Observed",  xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(fit$mkinmod$map), pch_obs = col_obs,  lty_obs = rep(1, length(fit$mkinmod$map)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", lpos = "topright", inset = c(0.05, 0.05), ...)
                                                  + 
                                                  "plot"(x, fit = x, obs_vars = names(fit$mkinmod$map), xlab = "Time", ylab = "Observed",  xlim = range(fit$data$time), ylim = "default", col_obs = 1:length(obs_vars), pch_obs = col_obs,  lty_obs = rep(1, length(obs_vars)), add = FALSE, legend = !add, show_residuals = FALSE, maxabs = "auto", sep_obs = FALSE, rel.height.middle = 0.9, lpos = "topright", inset = c(0.05, 0.05),  show_errmin = FALSE, errmin_digits = 3, ...)
+plot_sep(fit, sep_obs = TRUE,  show_residuals = TRUE, show_errmin = TRUE, ...)

                                                  Arguments

                                                  @@ -66,7 +67,7 @@
                                                  fit
                                                  - an object of class mkinfit. + An object of class mkinfit.
                                                  obs_vars
                                                  @@ -76,60 +77,81 @@
                                                  xlab
                                                  - label for the x axis. + Label for the x axis.
                                                  ylab
                                                  - label for the y axis. + Label for the y axis.
                                                  xlim
                                                  - plot range in x direction. + Plot range in x direction.
                                                  ylim
                                                  - plot range in y direction. + Plot range in y direction.
                                                  col_obs
                                                  - colors used for plotting the observed data and the corresponding model prediction lines. + Colors used for plotting the observed data and the corresponding model prediction lines.
                                                  pch_obs
                                                  - symbols to be used for plotting the data. + Symbols to be used for plotting the data.
                                                  lty_obs
                                                  - line types to be used for the model predictions. + Line types to be used for the model predictions.
                                                  add
                                                  - should the plot be added to an existing plot? + Should the plot be added to an existing plot?
                                                  legend
                                                  - should a legend be added to the plot? + Should a legend be added to the plot?
                                                  show_residuals
                                                  - should residuals be shown in the lower third of the plot? + Should residuals be shown? If only one plot of the fits is shown, the + residual plot is in the lower third of the plot? Otherwise, i.e. if + "sep_obs" is given, the residual plots will be located to the right of + the plots of the fitted curves.
                                                  maxabs
                                                  Maximum absolute value of the residuals. This is used for the scaling of the y axis and defaults to "auto". +
                                                  +
                                                  sep_obs
                                                  +
                                                  + Should the observed variables be shown in separate subplots? If yes, residual plots + requested by "show_residuals" will be shown next to, not below the plot of the fits. +
                                                  +
                                                  rel.height.middle
                                                  +
                                                  + The relative height of the middle plot, if more than two rows of plots are shown.
                                                  lpos
                                                  - position of the legend. Passed to legend as the first argument. + Position(s) of the legend(s). Passed to legend as the first argument. + If not length one, this should be of the same length as the obs_var argument.
                                                  inset
                                                  Passed to legend if applicable. +
                                                  +
                                                  show_errmin
                                                  +
                                                  + Should the FOCUS chi2 error value be shown in the upper margin of the plot? +
                                                  +
                                                  errmin_digits
                                                  +
                                                  + The number of significant digits for rounding the FOCUS chi2 error percentage.
                                                  ...
                                                  - further arguments passed to plot. + Further arguments passed to plot.
                                                  @@ -153,22 +175,40 @@

                                                  Examples

                                                  # One parent compound, one metabolite, both single first order, path from
-# parent to sink included
+# parent to sink included, use Levenberg-Marquardt for speed
 SFO_SFO <- mkinmod(parent = mkinsub("SFO", "m1", full = "Parent"),
                    m1 = mkinsub("SFO", full = "Metabolite M1" ))
 
                                                  
 Successfully compiled differential equation model from auto-generated C code.
-
                                                  fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
+
                                                  fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE, method.modFit = "Marq")
 plot(fit)
 
                                                  
-
                                                  +

                                                  +
                                                  plot(fit, show_residuals = TRUE) +
                                                  +

                                                  +
                                                  +# Show the observed variables separately +plot(fit, sep_obs = TRUE, lpos = c("topright", "bottomright")) +
                                                  +

                                                  +
                                                  +# Show the observed variables separately, with residuals +plot(fit, sep_obs = TRUE, show_residuals = TRUE, lpos = c("topright", "bottomright"), + show_errmin = TRUE) +
                                                  +

                                                  +
                                                  +# The same can be obtained with less typing, using the convenience function plot_sep +plot_sep(fit, lpos = c("topright", "bottomright")) +
                                                  diff --git a/inst/web/plot.mmkin-6.png b/inst/web/plot.mmkin-6.png new file mode 100644 index 00000000..f0282344 Binary files /dev/null and b/inst/web/plot.mmkin-6.png differ diff --git a/inst/web/plot.mmkin.html b/inst/web/plot.mmkin.html index 587bf894..1bc440e1 100644 --- a/inst/web/plot.mmkin.html +++ b/inst/web/plot.mmkin.html @@ -2,7 +2,7 @@ -plot.mmkin. mkin 0.9.42 +plot.mmkin. mkin 0.9.43
                                                  - mkin 0.9.42 + mkin 0.9.43
                                                  • Index
                                                    • @@ -56,7 +56,7 @@

                                                    Usage

                                                    - 
                                                    "plot"(x, main = "auto", legends = 1, errmin_var = "All data", errmin_digits = 2,  cex = 0.7, rel.height.middle = 0.9, ...)
                                                    + 
                                                    "plot"(x, main = "auto", legends = 1, errmin_var = "All data", errmin_digits = 3,  cex = 0.7, rel.height.middle = 0.9, ...)

                                                    Arguments

                                                    @@ -78,7 +78,7 @@
                                                    errmin_digits
                                                    - The number of digits for rounding the FOCUS chi2 error percentage. + The number of significant digits for rounding the FOCUS chi2 error percentage.
                                                    cex
                                                    @@ -86,7 +86,7 @@
                                                    rel.height.middle
                                                    - The relative height of the middle plot. + The relative height of the middle plot, if more than two rows of plots are shown.
                                                    ...
                                                    @@ -113,15 +113,22 @@

                                                    Examples

                                                    - 
                                                      # Only use one core not to offend CRAN checks
+    
                                                      # Only use one core not to offend CRAN checks, use Levenberg-Marquardt for speed
   fits <- mmkin(c("FOMC", "HS"), list("FOCUS B" = FOCUS_2006_B, "FOCUS C" = FOCUS_2006_C), 
-                cores = 1, quiet = TRUE)
+                cores = 1, quiet = TRUE, method.modFit = "Marq")
   plot(fits[, "FOCUS C"])
 
                                                    
 
                                                    
 
                                                      plot(fits["FOMC", ])
 
                                                    
-
                                                    
+
                                                    
+
                                                    
+  # We can also plot a single fit, if we like the way mmkin works, but then the plot 
+  # height should be smaller than the plot width (this is not possible for the html pages
+  # generated by staticdocs, as far as I know).
+  plot(fits["FOMC", "FOCUS C"]) # same as plot(fits[1, 2])
+
                                                    
+
                                                    + + + + + + + - + + + + - - + + - + @@ -38,7 +42,34 @@ if (window.hljs && document.readyState && document.readyState === "complete") { - + + + @@ -54,33 +85,144 @@ code { color: inherit; background-color: rgba(0, 0, 0, 0.04); } -img { - max-width:100%; - height: auto; +img { + max-width:100%; + height: auto; +} +.tabbed-pane { + padding-top: 12px; +} +button.code-folding-btn:focus { + outline: none; } + +
                                                    + + + -