From 6f596ecec2c54d7d91cf3ca16b8643b64b903e57 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Fri, 13 Nov 2015 11:01:49 +0100 Subject: Add plots to compiled_models vignette, rebuild staticdocs --- 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/endpoints.html | 4 +- inst/web/geometric_mean.html | 4 +- inst/web/ilr.html | 4 +- inst/web/index.html | 6 +-- inst/web/mccall81_245T.html | 12 ++--- 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 | 14 ++--- inst/web/mkinmod.html | 4 +- inst/web/mkinparplot.html | 4 +- inst/web/mkinplot.html | 4 +- inst/web/mkinpredict.html | 8 +-- inst/web/mkinresplot.html | 4 +- inst/web/mkinsub.html | 4 +- inst/web/mmkin.html | 4 +- inst/web/plot.mkinfit.html | 4 +- inst/web/plot.mmkin.html | 4 +- inst/web/print.mkinds.html | 4 +- inst/web/print.mkinmod.html | 4 +- inst/web/schaefer07_complex_case.html | 4 +- inst/web/summary.mkinfit.html | 12 ++--- inst/web/synthetic_data_for_UBA.html | 4 +- inst/web/transform_odeparms.html | 12 ++--- inst/web/vignettes/FOCUS_D.html | 4 +- inst/web/vignettes/FOCUS_L.html | 4 +- inst/web/vignettes/FOCUS_Z.pdf | Bin 224775 -> 224838 bytes inst/web/vignettes/compiled_models.html | 85 +++++++++++++++++-------------- inst/web/vignettes/mkin.pdf | Bin 160268 -> 160269 bytes 42 files changed, 158 insertions(+), 147 deletions(-) (limited to 'inst') diff --git a/inst/web/DFOP.solution.html b/inst/web/DFOP.solution.html index 87f3ea21..b5bdbc33 100644 --- a/inst/web/DFOP.solution.html +++ b/inst/web/DFOP.solution.html @@ -2,7 +2,7 @@ -DFOP.solution. mkin 0.9-41 +DFOP.solution. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
- mkin 0.9-41 + mkin 0.9.41.9000
  • Index
    • diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 6a175a02..4effdf0e 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -2,7 +2,7 @@ -[.mmkin. mkin 0.9-41 +[.mmkin. mkin 0.9.41.9000
    - mkin 0.9-41 + mkin 0.9.41.9000
    • Index
      • @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.268 0.000 0.269 + 0.260 0.000 0.259 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x2d96b00> +<environment: 0x36e8dd8> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x2d96b00> +<environment: 0x36e8dd8> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Mon Nov 9 10:11:49 2015" +[1] "Fri Nov 13 11:14:06 2015" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.112 0.000 0.112 + 0.080 0.008 0.087 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x2fa3d28> +<environment: 0x33c0330> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x2fa3d28> +<environment: 0x33c0330> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Mon Nov 9 10:11:48 2015" +[1] "Fri Nov 13 11:14:06 2015" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.112 0.000 0.112 + 0.080 0.008 0.087 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x2fa3d28> +<environment: 0x33c0330> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x2fa3d28> +<environment: 0x33c0330> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Mon Nov 9 10:11:48 2015" +[1] "Fri Nov 13 11:14:06 2015" 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 19ec4c4b..b009f6e6 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 0.9-41 +FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
      - mkin 0.9-41 + mkin 0.9.41.9000
      • 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 ff7883ec..c28cd888 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 0.9-41 +FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
        - mkin 0.9-41 + mkin 0.9.41.9000
        • 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 5786889a..ad779e12 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 0.9-41 +FOCUS_2006_HS_ref_A_to_F. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
          - mkin 0.9-41 + mkin 0.9.41.9000
          • 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 7663cb53..391aa699 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 0.9-41 +FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
            - mkin 0.9-41 + mkin 0.9.41.9000
            • Index
              • diff --git a/inst/web/FOCUS_2006_datasets.html b/inst/web/FOCUS_2006_datasets.html index 92e069b5..64ae3bd7 100644 --- a/inst/web/FOCUS_2006_datasets.html +++ b/inst/web/FOCUS_2006_datasets.html @@ -2,7 +2,7 @@ -FOCUS_2006_datasets. mkin 0.9-41 +FOCUS_2006_datasets. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
              - mkin 0.9-41 + mkin 0.9.41.9000
              • Index
                • diff --git a/inst/web/FOMC.solution.html b/inst/web/FOMC.solution.html index 0f3f265b..06d2d233 100644 --- a/inst/web/FOMC.solution.html +++ b/inst/web/FOMC.solution.html @@ -2,7 +2,7 @@ -FOMC.solution. mkin 0.9-41 +FOMC.solution. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                - mkin 0.9-41 + mkin 0.9.41.9000
                • Index
                  • diff --git a/inst/web/HS.solution.html b/inst/web/HS.solution.html index 80cc543b..b7573295 100644 --- a/inst/web/HS.solution.html +++ b/inst/web/HS.solution.html @@ -2,7 +2,7 @@ -HS.solution. mkin 0.9-41 +HS.solution. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                  - mkin 0.9-41 + mkin 0.9.41.9000
                  • Index
                    • diff --git a/inst/web/IORE.solution.html b/inst/web/IORE.solution.html index d90724eb..b2b60111 100644 --- a/inst/web/IORE.solution.html +++ b/inst/web/IORE.solution.html @@ -2,7 +2,7 @@ -IORE.solution. mkin 0.9-41 +IORE.solution. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                    - mkin 0.9-41 + mkin 0.9.41.9000
                    • Index
                      • diff --git a/inst/web/SFO.solution.html b/inst/web/SFO.solution.html index b7d81cb7..a30000d8 100644 --- a/inst/web/SFO.solution.html +++ b/inst/web/SFO.solution.html @@ -2,7 +2,7 @@ -SFO.solution. mkin 0.9-41 +SFO.solution. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                      - mkin 0.9-41 + mkin 0.9.41.9000
                      • Index
                        • diff --git a/inst/web/SFORB.solution.html b/inst/web/SFORB.solution.html index 9388a848..42c6baa9 100644 --- a/inst/web/SFORB.solution.html +++ b/inst/web/SFORB.solution.html @@ -2,7 +2,7 @@ -SFORB.solution. mkin 0.9-41 +SFORB.solution. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                        - mkin 0.9-41 + mkin 0.9.41.9000
                        • Index
                          • diff --git a/inst/web/endpoints.html b/inst/web/endpoints.html index 458d359c..8c9b557f 100644 --- a/inst/web/endpoints.html +++ b/inst/web/endpoints.html @@ -2,7 +2,7 @@ -endpoints. mkin 0.9-41 +endpoints. mkin 0.9.41.9000
                          - mkin 0.9-41 + mkin 0.9.41.9000
                          • Index
                            • diff --git a/inst/web/geometric_mean.html b/inst/web/geometric_mean.html index 93962dca..2323a337 100644 --- a/inst/web/geometric_mean.html +++ b/inst/web/geometric_mean.html @@ -2,7 +2,7 @@ -geometric_mean. mkin 0.9-41 +geometric_mean. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                            - mkin 0.9-41 + mkin 0.9.41.9000
                            • Index
                              • diff --git a/inst/web/ilr.html b/inst/web/ilr.html index 07076e73..b75c111f 100644 --- a/inst/web/ilr.html +++ b/inst/web/ilr.html @@ -2,7 +2,7 @@ -ilr. mkin 0.9-41 +ilr. mkin 0.9.41.9000
                              - mkin 0.9-41 + mkin 0.9.41.9000
                              • Index
                                • diff --git a/inst/web/index.html b/inst/web/index.html index 71fdee45..bb85e72f 100644 --- a/inst/web/index.html +++ b/inst/web/index.html @@ -2,7 +2,7 @@ -Index. mkin 0.9-41 +Index. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                                - mkin 0.9-41 + mkin 0.9.41.9000
                                • Index
                                  • @@ -430,7 +430,7 @@ You can also browse the source code at cgit.j
                                  • Depends: minpack.lm, rootSolve, inline, parallel
                                  • Imports: stats, graphics, methods, FME, deSolve, R6
                                    • -
                                  • Suggests: knitr, testthat, microbenchmark
                                    • +
                                  • Suggests: knitr, testthat, microbenchmark, ggplot2

                                  Authors

                                  diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index cd8d4d73..c959f114 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -2,7 +2,7 @@ -mccall81_245T. mkin 0.9-41 +mccall81_245T. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                                  - mkin 0.9-41 + mkin 0.9.41.9000
                                  • Index
                                    • @@ -112,10 +112,10 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
                                  -
                                  mkin version: 0.9.41 +
                                  mkin version: 0.9.41.9000 R version: 3.2.2 -Date of fit: Mon Nov 9 10:11:56 2015 -Date of summary: Mon Nov 9 10:11:56 2015 +Date of fit: Fri Nov 13 11:14:13 2015 +Date of summary: Fri Nov 13 11:14:13 2015 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 1.39 s +Fitted with method Port using 246 model solutions performed in 1.369 s Weighting: none diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index 7c459da7..3bb32a4d 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 0.9-41 +mkin_long_to_wide. mkin 0.9.41.9000
                                  - mkin 0.9-41 + mkin 0.9.41.9000
                                  • Index
                                    • diff --git a/inst/web/mkin_wide_to_long.html b/inst/web/mkin_wide_to_long.html index 57e3e8ef..82dba968 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 0.9-41 +mkin_wide_to_long. mkin 0.9.41.9000
                                    - mkin 0.9-41 + mkin 0.9.41.9000
                                    • Index
                                      • diff --git a/inst/web/mkinds.html b/inst/web/mkinds.html index 5ff5e40c..d883c8e0 100644 --- a/inst/web/mkinds.html +++ b/inst/web/mkinds.html @@ -2,7 +2,7 @@ -mkinds. mkin 0.9-41 +mkinds. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                                      - mkin 0.9-41 + mkin 0.9.41.9000
                                      • Index
                                        • diff --git a/inst/web/mkinerrmin.html b/inst/web/mkinerrmin.html index d8a90977..0aafc760 100644 --- a/inst/web/mkinerrmin.html +++ b/inst/web/mkinerrmin.html @@ -2,7 +2,7 @@ -mkinerrmin. mkin 0.9-41 +mkinerrmin. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                                        - mkin 0.9-41 + mkin 0.9.41.9000
                                        • Index
                                          • diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 0550ee65..c2998ae6 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -2,7 +2,7 @@ -mkinfit. mkin 0.9-41 +mkinfit. mkin 0.9.41.9000
                                          - mkin 0.9-41 + mkin 0.9.41.9000
                                          • Index
                                            • @@ -315,17 +315,17 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
                                          -
                                          mkin version: 0.9.41 +
                                          mkin version: 0.9.41.9000 R version: 3.2.2 -Date of fit: Mon Nov 9 10:11:58 2015 -Date of summary: Mon Nov 9 10:11:58 2015 +Date of fit: Fri Nov 13 11:14:16 2015 +Date of summary: Fri Nov 13 11:14:16 2015 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 0.194 s +Fitted with method Port using 64 model solutions performed in 0.171 s Weighting: none @@ -401,7 +401,7 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
                                          user system elapsed - 1.188 1.228 0.910 + 1.200 1.188 0.898
                                          coef(fit)
                                          diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index 7b43beb7..ea549f29 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9-41 +mkinmod. mkin 0.9.41.9000
                                          - mkin 0.9-41 + mkin 0.9.41.9000
                                          • Index
                                            • diff --git a/inst/web/mkinparplot.html b/inst/web/mkinparplot.html index 396e1428..8027af58 100644 --- a/inst/web/mkinparplot.html +++ b/inst/web/mkinparplot.html @@ -2,7 +2,7 @@ -mkinparplot. mkin 0.9-41 +mkinparplot. mkin 0.9.41.9000
                                            - mkin 0.9-41 + mkin 0.9.41.9000
                                            • Index
                                              • diff --git a/inst/web/mkinplot.html b/inst/web/mkinplot.html index 74c8c29f..c8787242 100644 --- a/inst/web/mkinplot.html +++ b/inst/web/mkinplot.html @@ -2,7 +2,7 @@ -mkinplot. mkin 0.9-41 +mkinplot. mkin 0.9.41.9000
                                              - mkin 0.9-41 + mkin 0.9.41.9000
                                              • Index
                                                • diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index 900ee26f..ee452a18 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -2,7 +2,7 @@ -mkinpredict. mkin 0.9-41 +mkinpredict. mkin 0.9.41.9000
                                                - mkin 0.9-41 + mkin 0.9.41.9000
                                                • Index
                                                  • @@ -315,7 +315,7 @@ 201 20 4.978707 27.46227
                                                user system elapsed - 0.020 0.000 0.003 + 0.016 0.004 0.002
                                                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 - 0.092 0.000 0.092 + 0.056 0.000 0.054
                                                diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index 579c047e..ec82518b 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9-41 +mkinresplot. mkin 0.9.41.9000
                                                - mkin 0.9-41 + mkin 0.9.41.9000
                                                • Index
                                                  • diff --git a/inst/web/mkinsub.html b/inst/web/mkinsub.html index 94e650ff..73b19907 100644 --- a/inst/web/mkinsub.html +++ b/inst/web/mkinsub.html @@ -2,7 +2,7 @@ -mkinsub. mkin 0.9-41 +mkinsub. mkin 0.9.41.9000
                                                  - mkin 0.9-41 + mkin 0.9.41.9000
                                                  • Index
                                                    • diff --git a/inst/web/mmkin.html b/inst/web/mmkin.html index e09e6859..cec39fc8 100644 --- a/inst/web/mmkin.html +++ b/inst/web/mmkin.html @@ -2,7 +2,7 @@ -mmkin. mkin 0.9-41 +mmkin. mkin 0.9.41.9000
                                                    - mkin 0.9-41 + mkin 0.9.41.9000
                                                    • Index
                                                      • diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html index 5308ecec..8acf1e19 100644 --- a/inst/web/plot.mkinfit.html +++ b/inst/web/plot.mkinfit.html @@ -2,7 +2,7 @@ -plot.mkinfit. mkin 0.9-41 +plot.mkinfit. mkin 0.9.41.9000
                                                      - mkin 0.9-41 + mkin 0.9.41.9000
                                                      • Index
                                                        • diff --git a/inst/web/plot.mmkin.html b/inst/web/plot.mmkin.html index 49b5d3af..11a1ba54 100644 --- a/inst/web/plot.mmkin.html +++ b/inst/web/plot.mmkin.html @@ -2,7 +2,7 @@ -plot.mmkin. mkin 0.9-41 +plot.mmkin. mkin 0.9.41.9000
                                                        - mkin 0.9-41 + mkin 0.9.41.9000
                                                        • Index
                                                          • diff --git a/inst/web/print.mkinds.html b/inst/web/print.mkinds.html index d2f5f806..fdaaa64a 100644 --- a/inst/web/print.mkinds.html +++ b/inst/web/print.mkinds.html @@ -2,7 +2,7 @@ -print.mkinds. mkin 0.9-41 +print.mkinds. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                                                          - mkin 0.9-41 + mkin 0.9.41.9000
                                                          • Index
                                                            • diff --git a/inst/web/print.mkinmod.html b/inst/web/print.mkinmod.html index dd94db34..457ac78f 100644 --- a/inst/web/print.mkinmod.html +++ b/inst/web/print.mkinmod.html @@ -2,7 +2,7 @@ -print.mkinmod. mkin 0.9-41 +print.mkinmod. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                                                            - mkin 0.9-41 + mkin 0.9.41.9000
                                                            • Index
                                                              • diff --git a/inst/web/schaefer07_complex_case.html b/inst/web/schaefer07_complex_case.html index 403e7229..e23bc962 100644 --- a/inst/web/schaefer07_complex_case.html +++ b/inst/web/schaefer07_complex_case.html @@ -2,7 +2,7 @@ -schaefer07_complex_case. mkin 0.9-41 +schaefer07_complex_case. mkin 0.9.41.9000 @@ -32,7 +32,7 @@
                                                              - mkin 0.9-41 + mkin 0.9.41.9000
                                                              • Index
                                                                • diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index 2958b020..1c63e7b9 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -2,7 +2,7 @@ -summary.mkinfit. mkin 0.9-41 +summary.mkinfit. mkin 0.9.41.9000
                                                                - mkin 0.9-41 + mkin 0.9.41.9000
                                                                • Index
                                                                  • @@ -157,17 +157,17 @@

                                                                  Examples

                                                                    summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
 
                                                                  
-
                                                                  mkin version:    0.9.41 
+
                                                                  mkin version:    0.9.41.9000 
 R version:       3.2.2 
-Date of fit:     Mon Nov  9 10:12:08 2015 
-Date of summary: Mon Nov  9 10:12:08 2015 
+Date of fit:     Fri Nov 13 11:14:26 2015 
+Date of summary: Fri Nov 13 11:14:26 2015 
 
 Equations:
 d_parent = - k_parent_sink * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 35 model solutions performed in 0.105 s
+Fitted with method Port using 35 model solutions performed in 0.151 s
 
 Weighting: none
 
diff --git a/inst/web/synthetic_data_for_UBA.html b/inst/web/synthetic_data_for_UBA.html
index 3694bcb9..2ae4c868 100644
--- a/inst/web/synthetic_data_for_UBA.html
+++ b/inst/web/synthetic_data_for_UBA.html
@@ -2,7 +2,7 @@
 
   
     
-synthetic_data_for_UBA_2014. mkin 0.9-41
+synthetic_data_for_UBA_2014. mkin 0.9.41.9000
 
 
 
@@ -32,7 +32,7 @@
     
                                                                  
   
                                                                  
     
                                                                  
-      mkin 0.9-41
+      mkin 0.9.41.9000
       
                                                                  
         
                                                                    
           
                                                                  •  Index
                                                                    • 
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index 36dfecf8..49639b47 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -2,7 +2,7 @@
 
   
     
-transform_odeparms. mkin 0.9-41
+transform_odeparms. mkin 0.9.41.9000
 
 
   
                                                                    
     
                                                                    
-      mkin 0.9-41
+      mkin 0.9.41.9000
       
                                                                    
         
                                                                      
           
                                                                    •  Index
                                                                      • 
@@ -133,10 +133,10 @@ backtransform_odeparms(transparms, mkinmod,  transform_rates = TRUE, t
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
 
                                                                    
-
                                                                    mkin version:    0.9.41 
+
                                                                    mkin version:    0.9.41.9000 
 R version:       3.2.2 
-Date of fit:     Mon Nov  9 10:12:09 2015 
-Date of summary: Mon Nov  9 10:12:09 2015 
+Date of fit:     Fri Nov 13 11:14:27 2015 
+Date of summary: Fri Nov 13 11:14:27 2015 
 
 Equations:
 d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -144,7 +144,7 @@ d_m1 = + k_parent_m1 * parent - k_m1_sink * m1
 
 Model predictions using solution type deSolve 
 
-Fitted with method Port using 153 model solutions performed in 0.632 s
+Fitted with method Port using 153 model solutions performed in 0.619 s
 
 Weighting: none
 
diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html
index 557ceb03..d9fc6e18 100644
--- a/inst/web/vignettes/FOCUS_D.html
+++ b/inst/web/vignettes/FOCUS_D.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Example Dataset D
 
@@ -64,7 +64,7 @@ img {
 
 
 
diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html
index 9bb60153..9584aee5 100644
--- a/inst/web/vignettes/FOCUS_L.html
+++ b/inst/web/vignettes/FOCUS_L.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Laboratory Data L1 to L3
 
@@ -65,7 +65,7 @@ img {
 
 
 
                                                                    
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index 31480019..1d08173a 100644
Binary files a/inst/web/vignettes/FOCUS_Z.pdf and b/inst/web/vignettes/FOCUS_Z.pdf differ
diff --git a/inst/web/vignettes/compiled_models.html b/inst/web/vignettes/compiled_models.html
index 7722d95a..c7f4fbea 100644
--- a/inst/web/vignettes/compiled_models.html
+++ b/inst/web/vignettes/compiled_models.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Performance benefit by using compiled model definitions in mkin
 
@@ -65,7 +65,7 @@ img {
 
 
 
                                                                    
@@ -89,28 +89,36 @@ SFO_SFO <- mkinmod(
 
                                                                    ## Successfully compiled differential equation model from auto-generated C code.
                                                                    
 
                                                                    We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the microbenchmark package.
                                                                    
 
                                                                    library("microbenchmark")
+library("ggplot2")
 mb.1 <- microbenchmark(
-  mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", use_compiled = FALSE, 
-          quiet = TRUE),
-  mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE),
-  mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet = TRUE),
+  "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
+                                    solution_type = "deSolve", 
+                                    use_compiled = FALSE, quiet = TRUE),
+  "Eigenvalue based" = mkinfit(SFO_SFO, FOCUS_2006_D, 
+                               solution_type = "eigen", quiet = TRUE),
+  "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
+                                solution_type = "deSolve", quiet = TRUE),
   times = 3, control = list(warmup = 1))
-smb.1 <- summary(mb.1)[-1]
-rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
-print(smb.1)
                                                                    
-
                                                                    ##                             min        lq      mean    median        uq
-## deSolve, not compiled 9442.5119 9447.2060 9458.3420 9451.9001 9466.2571
-## Eigenvalue based       868.6312  872.4552  895.3422  876.2792  908.6977
-## deSolve, compiled      691.9663  697.5653  701.1004  703.1643  705.6674
-##                             max neval cld
-## deSolve, not compiled 9480.6141     3   c
-## Eigenvalue based       941.1163     3  b 
-## deSolve, compiled      708.1706     3 a
                                                                    
-
                                                                    We see that using the compiled model is by a factor of 13.4 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:
                                                                    
-
                                                                    smb.1["median"]/smb.1["deSolve, compiled", "median"]
                                                                    
+
+smb.1 <- summary(mb.1)
+print(mb.1)
                                                                  +
                                                                  ## Unit: milliseconds
+##                   expr       min        lq      mean    median        uq
+##  deSolve, not compiled 9538.4007 9570.3211 9605.6503 9602.2416 9639.2752
+##       Eigenvalue based  881.9438  885.9337  901.1558  889.9236  910.7618
+##      deSolve, compiled  692.0913  695.6109  697.9629  699.1304  700.8987
+##        max neval cld
+##  9676.3087     3   c
+##   931.5999     3  b 
+##   702.6669     3 a
                                                                  +
                                                                  autoplot(mb.1)
                                                                  +

                                                                  +

                                                                  We see that using the compiled model is by a factor of 13.7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

                                                                  +
                                                                  rownames(smb.1) <- smb.1$expr
+smb.1["median"]/smb.1["deSolve, compiled", "median"]
                                                                  ##                          median
-## deSolve, not compiled 13.441951
-## Eigenvalue based       1.246194
+## deSolve, not compiled 13.734549
+## Eigenvalue based       1.272901
 ## deSolve, compiled      1.000000
                                                                @@ -121,24 +129,27 @@ print(smb.1) m1 = mkinsub( "SFO")) 
                                                                ## Successfully compiled differential equation model from auto-generated C code.
                                                                mb.2 <- microbenchmark(
-  mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE),
-  mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
+  "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, 
+                                    use_compiled = FALSE, quiet = TRUE),
+  "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
   times = 3, control = list(warmup = 1))
-smb.2 <- summary(mb.2)[-1]
-rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled")
-print(smb.2)
                                                                -
                                                                ##                             min       lq      mean    median        uq
-## deSolve, not compiled 20.444632 20.48824 20.557595 20.531857 20.614077
-## deSolve, compiled      1.251733  1.25179  1.275227  1.251846  1.286973
-##                           max neval cld
-## deSolve, not compiled 20.6963     3   b
-## deSolve, compiled      1.3221     3  a
                                                                +smb.2 <- summary(mb.2) +print(mb.2) +
                                                                ## Unit: seconds
+##                   expr       min        lq      mean    median        uq
+##  deSolve, not compiled 20.475764 20.494740 20.507391 20.513716 20.523205
+##      deSolve, compiled  1.244022  1.244327  1.261983  1.244631  1.270963
+##        max neval cld
+##  20.532695     3   b
+##   1.297295     3  a
                                                                smb.2["median"]/smb.2["deSolve, compiled", "median"]
                                                                -
                                                                ##                         median
-## deSolve, not compiled 16.40126
-## deSolve, compiled      1.00000
                                                                -

                                                                Here we get a performance benefit of a factor of 16.4 using the version of the differential equation model compiled from C code using the inline package!

                                                                -

                                                                This vignette was built with mkin 0.9.41 on

                                                                +
                                                                ##   median
+## 1     NA
+## 2     NA
                                                                +
                                                                autoplot(mb.2)
                                                                +

                                                                +

                                                                Here we get a performance benefit of a factor of 16.5 using the version of the differential equation model compiled from C code using the inline package!

                                                                +

                                                                This vignette was built with mkin 0.9.41.9000 on

                                                                ## R version 3.2.2 (2015-08-14)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)
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