From 7faf98ac5475bb2041d7e434478c58c2f2cec0fd Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Jun 2016 08:23:38 +0200 Subject: Static documentation rebuilt by staticdocs::build_site() --- 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.html | 4 +- inst/web/endpoints.html | 4 +- inst/web/geometric_mean.html | 4 +- inst/web/ilr.html | 4 +- inst/web/index.html | 4 +- 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 | 10 ++--- inst/web/synthetic_data_for_UBA.html | 4 +- inst/web/transform_odeparms.html | 12 ++--- inst/web/vignettes/FOCUS_D.html | 12 ++--- inst/web/vignettes/FOCUS_L.html | 74 +++++++++++++++---------------- inst/web/vignettes/FOCUS_Z.pdf | Bin 238788 -> 238788 bytes inst/web/vignettes/compiled_models.html | 38 ++++++++-------- inst/web/vignettes/mkin.html | 2 +- vignettes/FOCUS_D.html | 17 +++---- vignettes/FOCUS_L.html | 56 +++++++++++------------ vignettes/FOCUS_Z.pdf | Bin 238788 -> 238788 bytes vignettes/compiled_models.html | 51 ++++++++++----------- vignettes/mkin.html | 10 +---- 48 files changed, 228 insertions(+), 244 deletions(-) diff --git a/inst/web/DFOP.solution.html b/inst/web/DFOP.solution.html index 4746beef..f9fc1ea8 100644 --- a/inst/web/DFOP.solution.html +++ b/inst/web/DFOP.solution.html @@ -2,7 +2,7 @@ -DFOP.solution. mkin 0.9.43 +DFOP.solution. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
- mkin 0.9.43 + mkin 0.9.43.9000
  • Index
    • diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index d165e11a..71d5957b 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -2,7 +2,7 @@ -[.mmkin. mkin 0.9.43 +[.mmkin. mkin 0.9.43.9000
    - mkin 0.9.43 + mkin 0.9.43.9000
    • Index
      • @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.712 0.000 0.711 + 0.696 0.000 0.698 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x498a868> +<environment: 0x3b92678> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x498a868> +<environment: 0x3b92678> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Tue Jun 28 01:54:25 2016" +[1] "Tue Jun 28 08:14:11 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.224 0.000 0.224 + 0.256 0.000 0.253 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x5658dc0> +<environment: 0x41e0de0> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x5658dc0> +<environment: 0x41e0de0> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 01:54:24 2016" +[1] "Tue Jun 28 08:14:11 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.224 0.000 0.224 + 0.256 0.000 0.253 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x5658dc0> +<environment: 0x41e0de0> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x5658dc0> +<environment: 0x41e0de0> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 01:54:24 2016" +[1] "Tue Jun 28 08:14:11 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 e5dad993..f3a19618 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 0.9.43 +FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
      - mkin 0.9.43 + mkin 0.9.43.9000
      • 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 ce238c92..84941896 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 0.9.43 +FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
        - mkin 0.9.43 + mkin 0.9.43.9000
        • 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 a1abc1b6..b79dd2d3 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 0.9.43 +FOCUS_2006_HS_ref_A_to_F. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
          - mkin 0.9.43 + mkin 0.9.43.9000
          • 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 badb4c41..fc7191b5 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 0.9.43 +FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
            - mkin 0.9.43 + mkin 0.9.43.9000
            • Index
              • diff --git a/inst/web/FOCUS_2006_datasets.html b/inst/web/FOCUS_2006_datasets.html index 7aa7f78b..4c87b181 100644 --- a/inst/web/FOCUS_2006_datasets.html +++ b/inst/web/FOCUS_2006_datasets.html @@ -2,7 +2,7 @@ -FOCUS_2006_datasets. mkin 0.9.43 +FOCUS_2006_datasets. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
              - mkin 0.9.43 + mkin 0.9.43.9000
              • Index
                • diff --git a/inst/web/FOMC.solution.html b/inst/web/FOMC.solution.html index 5c17afe4..ae9f60f0 100644 --- a/inst/web/FOMC.solution.html +++ b/inst/web/FOMC.solution.html @@ -2,7 +2,7 @@ -FOMC.solution. mkin 0.9.43 +FOMC.solution. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                - mkin 0.9.43 + mkin 0.9.43.9000
                • Index
                  • diff --git a/inst/web/HS.solution.html b/inst/web/HS.solution.html index 7f84cccd..593b2fb4 100644 --- a/inst/web/HS.solution.html +++ b/inst/web/HS.solution.html @@ -2,7 +2,7 @@ -HS.solution. mkin 0.9.43 +HS.solution. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                  - mkin 0.9.43 + mkin 0.9.43.9000
                  • Index
                    • diff --git a/inst/web/IORE.solution.html b/inst/web/IORE.solution.html index f735b3ad..825ae816 100644 --- a/inst/web/IORE.solution.html +++ b/inst/web/IORE.solution.html @@ -2,7 +2,7 @@ -IORE.solution. mkin 0.9.43 +IORE.solution. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                    - mkin 0.9.43 + mkin 0.9.43.9000
                    • Index
                      • diff --git a/inst/web/SFO.solution.html b/inst/web/SFO.solution.html index 2f0d2ff1..ca866ddc 100644 --- a/inst/web/SFO.solution.html +++ b/inst/web/SFO.solution.html @@ -2,7 +2,7 @@ -SFO.solution. mkin 0.9.43 +SFO.solution. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                      - mkin 0.9.43 + mkin 0.9.43.9000
                      • Index
                        • diff --git a/inst/web/SFORB.solution.html b/inst/web/SFORB.solution.html index 0285188b..74e7370c 100644 --- a/inst/web/SFORB.solution.html +++ b/inst/web/SFORB.solution.html @@ -2,7 +2,7 @@ -SFORB.solution. mkin 0.9.43 +SFORB.solution. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                        - mkin 0.9.43 + mkin 0.9.43.9000
                        • Index
                          • diff --git a/inst/web/add_err.html b/inst/web/add_err.html index 67ff8f70..da3a85b7 100644 --- a/inst/web/add_err.html +++ b/inst/web/add_err.html @@ -2,7 +2,7 @@ -add_err. mkin 0.9.43 +add_err. mkin 0.9.43.9000
                          - mkin 0.9.43 + mkin 0.9.43.9000
                          • Index
                            • diff --git a/inst/web/endpoints.html b/inst/web/endpoints.html index 0566d93f..b57874e3 100644 --- a/inst/web/endpoints.html +++ b/inst/web/endpoints.html @@ -2,7 +2,7 @@ -endpoints. mkin 0.9.43 +endpoints. mkin 0.9.43.9000
                            - mkin 0.9.43 + mkin 0.9.43.9000
                            • Index
                              • diff --git a/inst/web/geometric_mean.html b/inst/web/geometric_mean.html index 82caad0e..a0c7610e 100644 --- a/inst/web/geometric_mean.html +++ b/inst/web/geometric_mean.html @@ -2,7 +2,7 @@ -geometric_mean. mkin 0.9.43 +geometric_mean. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                              - mkin 0.9.43 + mkin 0.9.43.9000
                              • Index
                                • diff --git a/inst/web/ilr.html b/inst/web/ilr.html index bcf1fc26..6c446569 100644 --- a/inst/web/ilr.html +++ b/inst/web/ilr.html @@ -2,7 +2,7 @@ -ilr. mkin 0.9.43 +ilr. mkin 0.9.43.9000
                                - mkin 0.9.43 + mkin 0.9.43.9000
                                • Index
                                  • diff --git a/inst/web/index.html b/inst/web/index.html index c04d674d..896373f2 100644 --- a/inst/web/index.html +++ b/inst/web/index.html @@ -2,7 +2,7 @@ -Index. mkin 0.9.43 +Index. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                                  - mkin 0.9.43 + mkin 0.9.43.9000
                                  • Index
                                    • diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 20328b34..335af648 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -2,7 +2,7 @@ -mccall81_245T. mkin 0.9.43 +mccall81_245T. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                                    - mkin 0.9.43 + mkin 0.9.43.9000
                                    • Index
                                      • @@ -112,10 +112,10 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
                                    -
                                    mkin version: 0.9.43 +
                                    mkin version: 0.9.43.9000 R version: 3.3.1 -Date of fit: Tue Jun 28 01:54:43 2016 -Date of summary: Tue Jun 28 01:54:43 2016 +Date of fit: Tue Jun 28 08:14:29 2016 +Date of summary: Tue Jun 28 08:14:29 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 3.74 s +Fitted with method Port using 246 model solutions performed in 3.812 s Weighting: none diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index e58ce305..8ce17568 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 0.9.43 +mkin_long_to_wide. mkin 0.9.43.9000
                                    - mkin 0.9.43 + mkin 0.9.43.9000
                                    • Index
                                      • diff --git a/inst/web/mkin_wide_to_long.html b/inst/web/mkin_wide_to_long.html index ab4f7dbb..fbc468fe 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 0.9.43 +mkin_wide_to_long. mkin 0.9.43.9000
                                      - mkin 0.9.43 + mkin 0.9.43.9000
                                      • Index
                                        • diff --git a/inst/web/mkinds.html b/inst/web/mkinds.html index f89128bf..5db3b179 100644 --- a/inst/web/mkinds.html +++ b/inst/web/mkinds.html @@ -2,7 +2,7 @@ -mkinds. mkin 0.9.43 +mkinds. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                                        - mkin 0.9.43 + mkin 0.9.43.9000
                                        • Index
                                          • diff --git a/inst/web/mkinerrmin.html b/inst/web/mkinerrmin.html index ba665376..b82caae8 100644 --- a/inst/web/mkinerrmin.html +++ b/inst/web/mkinerrmin.html @@ -2,7 +2,7 @@ -mkinerrmin. mkin 0.9.43 +mkinerrmin. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                                          - mkin 0.9.43 + mkin 0.9.43.9000
                                          • Index
                                            • diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 9e0162c5..2d13317a 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -2,7 +2,7 @@ -mkinfit. mkin 0.9.43 +mkinfit. mkin 0.9.43.9000
                                            - mkin 0.9.43 + mkin 0.9.43.9000
                                            • Index
                                              • @@ -323,17 +323,17 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
                                            -
                                            mkin version: 0.9.43 +
                                            mkin version: 0.9.43.9000 R version: 3.3.1 -Date of fit: Tue Jun 28 01:54:49 2016 -Date of summary: Tue Jun 28 01:54:49 2016 +Date of fit: Tue Jun 28 08:14:35 2016 +Date of summary: Tue Jun 28 08:14:35 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 0.433 s +Fitted with method Port using 64 model solutions performed in 0.438 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 - 2.788 2.280 2.257 + 2.788 2.244 2.238
                                            coef(fit)
                                            diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index 0a361956..714975c1 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9.43 +mkinmod. mkin 0.9.43.9000
                                            - mkin 0.9.43 + mkin 0.9.43.9000
                                            • Index
                                              • diff --git a/inst/web/mkinparplot.html b/inst/web/mkinparplot.html index 59fddb39..e5a91e3a 100644 --- a/inst/web/mkinparplot.html +++ b/inst/web/mkinparplot.html @@ -2,7 +2,7 @@ -mkinparplot. mkin 0.9.43 +mkinparplot. mkin 0.9.43.9000
                                              - mkin 0.9.43 + mkin 0.9.43.9000
                                              • Index
                                                • diff --git a/inst/web/mkinplot.html b/inst/web/mkinplot.html index 1b9a8a02..3a45bea8 100644 --- a/inst/web/mkinplot.html +++ b/inst/web/mkinplot.html @@ -2,7 +2,7 @@ -mkinplot. mkin 0.9.43 +mkinplot. mkin 0.9.43.9000
                                                - mkin 0.9.43 + mkin 0.9.43.9000
                                                • Index
                                                  • diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index be761407..718aad5d 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -2,7 +2,7 @@ -mkinpredict. mkin 0.9.43 +mkinpredict. mkin 0.9.43.9000
                                                  - mkin 0.9.43 + mkin 0.9.43.9000
                                                  • Index
                                                    • @@ -315,7 +315,7 @@ 201 20 4.978707 27.46227
                                                  user system elapsed - 0.024 0.000 0.005 + 0.000 0.004 0.004
                                                  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 - 0.140 0.000 0.139 + 0.136 0.004 0.138
                                                  diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index b5f32633..6619c0b9 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9.43 +mkinresplot. mkin 0.9.43.9000
                                                  - mkin 0.9.43 + mkin 0.9.43.9000
                                                  • Index
                                                    • diff --git a/inst/web/mkinsub.html b/inst/web/mkinsub.html index bd8e1de6..1c7ca30a 100644 --- a/inst/web/mkinsub.html +++ b/inst/web/mkinsub.html @@ -2,7 +2,7 @@ -mkinsub. mkin 0.9.43 +mkinsub. mkin 0.9.43.9000
                                                    - mkin 0.9.43 + mkin 0.9.43.9000
                                                    • Index
                                                      • diff --git a/inst/web/mmkin.html b/inst/web/mmkin.html index b3e7a6fd..f600ffd3 100644 --- a/inst/web/mmkin.html +++ b/inst/web/mmkin.html @@ -2,7 +2,7 @@ -mmkin. mkin 0.9.43 +mmkin. mkin 0.9.43.9000
                                                      - mkin 0.9.43 + mkin 0.9.43.9000
                                                      • Index
                                                        • diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html index 9642b345..6a37657f 100644 --- a/inst/web/plot.mkinfit.html +++ b/inst/web/plot.mkinfit.html @@ -2,7 +2,7 @@ -plot.mkinfit. mkin 0.9.43 +plot.mkinfit. mkin 0.9.43.9000
                                                        - mkin 0.9.43 + mkin 0.9.43.9000
                                                        • Index
                                                          • diff --git a/inst/web/plot.mmkin.html b/inst/web/plot.mmkin.html index 1bc440e1..c12f92f2 100644 --- a/inst/web/plot.mmkin.html +++ b/inst/web/plot.mmkin.html @@ -2,7 +2,7 @@ -plot.mmkin. mkin 0.9.43 +plot.mmkin. mkin 0.9.43.9000
                                                          - mkin 0.9.43 + mkin 0.9.43.9000
                                                          • Index
                                                            • diff --git a/inst/web/print.mkinds.html b/inst/web/print.mkinds.html index 6ff9e02a..523e1e67 100644 --- a/inst/web/print.mkinds.html +++ b/inst/web/print.mkinds.html @@ -2,7 +2,7 @@ -print.mkinds. mkin 0.9.43 +print.mkinds. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                                                            - mkin 0.9.43 + mkin 0.9.43.9000
                                                            • Index
                                                              • diff --git a/inst/web/print.mkinmod.html b/inst/web/print.mkinmod.html index 16c59669..ca4e5d36 100644 --- a/inst/web/print.mkinmod.html +++ b/inst/web/print.mkinmod.html @@ -2,7 +2,7 @@ -print.mkinmod. mkin 0.9.43 +print.mkinmod. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                                                              - mkin 0.9.43 + mkin 0.9.43.9000
                                                              • Index
                                                                • diff --git a/inst/web/schaefer07_complex_case.html b/inst/web/schaefer07_complex_case.html index f2975fe6..2e5d91a2 100644 --- a/inst/web/schaefer07_complex_case.html +++ b/inst/web/schaefer07_complex_case.html @@ -2,7 +2,7 @@ -schaefer07_complex_case. mkin 0.9.43 +schaefer07_complex_case. mkin 0.9.43.9000 @@ -32,7 +32,7 @@
                                                                - mkin 0.9.43 + mkin 0.9.43.9000
                                                                • Index
                                                                  • diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index 724e470d..fade0f56 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -2,7 +2,7 @@ -summary.mkinfit. mkin 0.9.43 +summary.mkinfit. mkin 0.9.43.9000
                                                                  - mkin 0.9.43 + mkin 0.9.43.9000
                                                                  • Index
                                                                    • @@ -157,10 +157,10 @@

                                                                    Examples

                                                                      summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
 
                                                                    
-
                                                                    mkin version:    0.9.43 
+
                                                                    mkin version:    0.9.43.9000 
 R version:       3.3.1 
-Date of fit:     Tue Jun 28 01:55:10 2016 
-Date of summary: Tue Jun 28 01:55:10 2016 
+Date of fit:     Tue Jun 28 08:14:56 2016 
+Date of summary: Tue Jun 28 08:14:56 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent
diff --git a/inst/web/synthetic_data_for_UBA.html b/inst/web/synthetic_data_for_UBA.html
index 56a646c1..2daf00ff 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 0.9.43
+synthetic_data_for_UBA_2014. mkin 0.9.43.9000
 
 
 
@@ -32,7 +32,7 @@
     
                                                                    
   
                                                                    
     
                                                                    
-      mkin 0.9.43
+      mkin 0.9.43.9000
       
                                                                    
         
                                                                      
           
                                                                    •  Index
                                                                      • 
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index aa7e22f3..50dd8ad4 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -2,7 +2,7 @@
 
   
     
-transform_odeparms. mkin 0.9.43
+transform_odeparms. mkin 0.9.43.9000
 
 
   
                                                                      
     
                                                                      
-      mkin 0.9.43
+      mkin 0.9.43.9000
       
                                                                      
         
                                                                        
           
                                                                      •  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:    0.9.43 
+
                                                                      mkin version:    0.9.43.9000 
 R version:       3.3.1 
-Date of fit:     Tue Jun 28 01:55:12 2016 
-Date of summary: Tue Jun 28 01:55:12 2016 
+Date of fit:     Tue Jun 28 08:14:58 2016 
+Date of summary: Tue Jun 28 08:14:58 2016 
 
 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 1.624 s
+Fitted with method Port using 153 model solutions performed in 1.67 s
 
 Weighting: none
 
diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html
index e01c5869..c7e2047f 100644
--- a/inst/web/vignettes/FOCUS_D.html
+++ b/inst/web/vignettes/FOCUS_D.html
@@ -184,16 +184,16 @@ print(FOCUS_2006_D)
                                                                    fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)

                                                                    A plot of the fit including a residual plot for both observed variables is obtained using the plot method for mkinfit objects.

                                                                    plot(fit, show_residuals = TRUE)
                                                                    -

                                                                    +

                                                                    Confidence intervals for the parameter estimates are obtained using the mkinparplot function.

                                                                    mkinparplot(fit)
                                                                    -

                                                                    +

                                                                    A comprehensive report of the results is obtained using the summary method for mkinfit objects.

                                                                    summary(fit)
                                                                    -
                                                                    ## mkin version:    0.9.43 
+
                                                                    ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:43 2016 
-## Date of summary: Tue Jun 28 01:59:44 2016 
+## Date of fit:     Tue Jun 28 08:19:31 2016 
+## Date of summary: Tue Jun 28 08:19:31 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -201,7 +201,7 @@ print(FOCUS_2006_D)
                                                                    
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 1.698 s
+## Fitted with method Port using 153 model solutions performed in 1.706 s
 ## 
 ## Weighting: none
 ## 
diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html
index 828d9def..05b9bdbd 100644
--- a/inst/web/vignettes/FOCUS_L.html
+++ b/inst/web/vignettes/FOCUS_L.html
@@ -233,17 +233,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

                                                                    Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

                                                                    m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
                                                                    -
                                                                    ## mkin version:    0.9.43 
+
                                                                    ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:45 2016 
-## Date of summary: Tue Jun 28 01:59:45 2016 
+## Date of fit:     Tue Jun 28 08:19:32 2016 
+## Date of summary: Tue Jun 28 08:19:32 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.243 s
+## Fitted with method Port using 37 model solutions performed in 0.245 s
 ## 
 ## Weighting: none
 ## 
@@ -315,21 +315,21 @@ summary(m.L1.SFO)
                                                                    
 ##    30   parent      4.0     5.251  -1.2513

                                                                    A plot of the fit is obtained with the plot function for mkinfit objects.

                                                                    plot(m.L1.SFO, show_errmin = TRUE, main = "FOCUS L1 - SFO")
                                                                    -

                                                                    +

                                                                    The residual plot can be easily obtained by

                                                                    mkinresplot(m.L1.SFO, ylab = "Observed", xlab = "Time")
                                                                    -

                                                                    +

                                                                    For comparison, the FOMC model is fitted as well, and the χ2 error level is checked.

                                                                    m.L1.FOMC <- mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet=TRUE)
                                                                    ## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
 ## Convergence code is 1
                                                                    plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
                                                                    -

                                                                    +

                                                                    summary(m.L1.FOMC, data = FALSE)
                                                                    -
                                                                    ## mkin version:    0.9.43 
+
                                                                    ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:47 2016 
-## Date of summary: Tue Jun 28 01:59:47 2016 
+## Date of fit:     Tue Jun 28 08:19:34 2016 
+## Date of summary: Tue Jun 28 08:19:34 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -341,7 +341,7 @@ summary(m.L1.SFO)
                                                                    
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 1.241 s
+## Fitted with method Port using 188 model solutions performed in 1.216 s
 ## 
 ## Weighting: none
 ## 
@@ -410,7 +410,7 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)
                                                                    m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
 plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE, 
      main = "FOCUS L2 - SFO")
                                                                    -

                                                                    +

                                                                    The χ2 error level of 14% suggests that the model does not fit very well. This is also obvious from the plots of the fit, in which we have included the residual plot.

                                                                    In the FOCUS kinetics report, it is stated that there is no apparent systematic error observed from the residual plot up to the measured DT90 (approximately at day 5), and there is an underestimation beyond that point.

                                                                    We may add that it is difficult to judge the random nature of the residuals just from the three samplings at days 0, 1 and 3. Also, it is not clear a priori why a consistent underestimation after the approximate DT90 should be irrelevant. However, this can be rationalised by the fact that the FOCUS fate models generally only implement SFO kinetics.

                                                                    @@ -421,19 +421,19 @@ plot(m.L2.SFO, show_residuals = TRUE, show_errmin = TRUE, 
                                                                    m.L2.FOMC <- mkinfit("FOMC", FOCUS_2006_L2_mkin, quiet = TRUE)
 plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")
                                                                    -

                                                                    +

                                                                    summary(m.L2.FOMC, data = FALSE)
                                                                    -
                                                                    ## mkin version:    0.9.43 
+
                                                                    ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:49 2016 
-## Date of summary: Tue Jun 28 01:59:49 2016 
+## Date of fit:     Tue Jun 28 08:19:36 2016 
+## Date of summary: Tue Jun 28 08:19:36 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.534 s
+## Fitted with method Port using 81 model solutions performed in 0.537 s
 ## 
 ## Weighting: none
 ## 
@@ -491,12 +491,12 @@ plot(m.L2.FOMC, show_residuals = TRUE,
 
                                                                    m.L2.DFOP <- mkinfit("DFOP", FOCUS_2006_L2_mkin, quiet = TRUE)
 plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")
                                                                    
-
                                                                    
+
                                                                    
 
                                                                    summary(m.L2.DFOP, data = FALSE)
                                                                    
-
                                                                    ## mkin version:    0.9.43 
+
                                                                    ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:52 2016 
-## Date of summary: Tue Jun 28 01:59:52 2016 
+## Date of fit:     Tue Jun 28 08:19:39 2016 
+## Date of summary: Tue Jun 28 08:19:39 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -505,7 +505,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 2.286 s
+## Fitted with method Port using 336 model solutions performed in 2.267 s
 ## 
 ## Weighting: none
 ## 
@@ -574,7 +574,7 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3)
                                                                    
 mm.L3 <- mmkin(c("SFO", "FOMC", "DFOP"), cores = 1,
                list("FOCUS L3" = FOCUS_2006_L3_mkin), quiet = TRUE)
 plot(mm.L3)
                                                                    
-
                                                                    
+
                                                                    
 
                                                                    The χ2 error level of 21% as well as the plot suggest that the SFO model does not fit very well. The FOMC model performs better, with an error level at which the χ2 test passes of 7%. Fitting the four parameter DFOP model further reduces the χ2 error level considerably.
                                                                  @@ -582,10 +582,10 @@ plot(mm.L3)

                                                                  The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.

                                                                  We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.

                                                                  summary(mm.L3[["DFOP", 1]])
                                                                  -
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:55 2016 
-## Date of summary: Tue Jun 28 01:59:56 2016 
+## Date of fit:     Tue Jun 28 08:19:41 2016 
+## Date of summary: Tue Jun 28 08:19:42 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -594,7 +594,7 @@ plot(mm.L3)
                                                                  
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.907 s
+## Fitted with method Port using 137 model solutions performed in 0.924 s
 ## 
 ## Weighting: none
 ## 
@@ -661,7 +661,7 @@ plot(mm.L3)
                                                                  ## 91 parent 15.0 15.18 -0.18181 ## 120 parent 12.0 10.19 1.81395 
                                                                  plot(mm.L3[["DFOP", 1]], show_errmin = TRUE)
                                                                  -

                                                                  +

                                                                  Here, a look to the model plot, the confidence intervals of the parameters and the correlation matrix suggest that the parameter estimates are reliable, and the DFOP model can be used as the best-fit model based on the χ2 error level criterion for laboratory data L3.

                                                                  This is also an example where the standard t-test for the parameter g_ilr is misleading, as it tests for a significant difference from zero. In this case, zero appears to be the correct value for this parameter, and the confidence interval for the backtransformed parameter g is quite narrow.

                                                                  @@ -679,20 +679,20 @@ mm.L4 <- mmkin(c("SFO", "FOMC"), cores = 1, list("FOCUS L4" = FOCUS_2006_L4_mkin), quiet = TRUE) plot(mm.L4) -

                                                                  +

                                                                  The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.

                                                                  summary(mm.L4[["SFO", 1]], data = FALSE)
                                                                  -
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:57 2016 
-## Date of summary: Tue Jun 28 01:59:58 2016 
+## Date of fit:     Tue Jun 28 08:19:42 2016 
+## Date of summary: Tue Jun 28 08:19:43 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.306 s
+## Fitted with method Port using 46 model solutions performed in 0.307 s
 ## 
 ## Weighting: none
 ## 
@@ -742,17 +742,17 @@ plot(mm.L4)
                                                                  
 ##        DT50 DT90
 ## parent  106  352
                                                                  summary(mm.L4[["FOMC", 1]], data = FALSE)
                                                                  -
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 01:59:57 2016 
-## Date of summary: Tue Jun 28 01:59:58 2016 
+## Date of fit:     Tue Jun 28 08:19:43 2016 
+## Date of summary: Tue Jun 28 08:19:43 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.42 s
+## Fitted with method Port using 66 model solutions performed in 0.414 s
 ## 
 ## Weighting: none
 ## 
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index efda950f..1f9560b0 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 5e426a7f..cec76ef9 100644
--- a/inst/web/vignettes/compiled_models.html
+++ b/inst/web/vignettes/compiled_models.html
@@ -20,7 +20,7 @@
 
 
 
-
+
 
 
 
@@ -250,21 +250,21 @@ mb.1 <- microbenchmark(
 print(mb.1)
                                                                  
 
                                                                  ## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 25.042204 25.078629 25.467550 25.115054 25.680223
-##       Eigenvalue based  2.273059  2.277424  2.285719  2.281790  2.292049
-##      deSolve, compiled  1.878785  1.883750  1.891594  1.888716  1.897998
-##        max neval cld
-##  26.245391     3   b
-##   2.302308     3  a 
-##   1.907281     3  a
                                                                  
+##  deSolve, not compiled 25.422123 25.889685 26.065978 26.357247 26.387905
+##       Eigenvalue based  2.243667  2.254539  2.277770  2.265412  2.294821
+##      deSolve, compiled  1.849468  1.865343  1.871339  1.881219  1.882274
+##       max neval cld
+##  26.41856     3   b
+##   2.32423     3  a 
+##   1.88333     3  a
                                                                  autoplot(mb.1)
                                                                  -

                                                                  -

                                                                  We see that using the compiled model is by a factor of 13.3 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:

                                                                  +

                                                                  +

                                                                  We see that using the compiled model is by a factor of 14 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 13.297425
-## Eigenvalue based       1.208117
+## deSolve, not compiled 14.010730
+## Eigenvalue based       1.204226
 ## deSolve, compiled      1.000000
                                                                  @@ -285,20 +285,20 @@ smb.1["median"]/smb.1["deSolve, compiled", "median" 
                                                                  smb.2 <- summary(mb.2)
 print(mb.2)
                                                                  ## Unit: seconds
-##                   expr      min        lq      mean    median        uq
-##  deSolve, not compiled 53.69252 53.938844 54.137601 54.185167 54.360141
-##      deSolve, compiled  3.42508  3.526298  3.588392  3.627516  3.670048
+##                   expr       min       lq      mean    median        uq
+##  deSolve, not compiled 54.386189 54.39423 54.477986 54.402271 54.523884
+##      deSolve, compiled  3.424205  3.53522  3.574587  3.646236  3.649778
 ##        max neval cld
-##  54.535116     3   b
-##   3.712579     3  a
                                                                  +## 54.645498 3 b +## 3.653319 3 a 
                                                                  smb.2["median"]/smb.2["deSolve, compiled", "median"]
                                                                  ##   median
 ## 1     NA
 ## 2     NA
                                                                  autoplot(mb.2)
                                                                  -

                                                                  +

                                                                  Here we get a performance benefit of a factor of 14.9 using the version of the differential equation model compiled from C code!

                                                                  -

                                                                  This vignette was built with mkin 0.9.43 on

                                                                  +

                                                                  This vignette was built with mkin 0.9.43.9000 on

                                                                  ## R version 3.3.1 (2016-06-21)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)
                                                                  diff --git a/inst/web/vignettes/mkin.html b/inst/web/vignettes/mkin.html index 9a76dc48..f9704eda 100644 --- a/inst/web/vignettes/mkin.html +++ b/inst/web/vignettes/mkin.html @@ -256,7 +256,7 @@ d_SFO_SFO_SFO_err <- add_err(d_SFO_SFO_SFO, function(x) 3, n = 1, seed = 1234 f_SFO_SFO_SFO <- mkinfit(m_SFO_SFO_SFO, d_SFO_SFO_SFO_err[[1]], quiet = TRUE) plot_sep(f_SFO_SFO_SFO, lpos = c("topright", "bottomright", "bottomright")) -

                                                                  +

                                                                  Background

                                                                  diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html index f3eb6a0c..c7e2047f 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -124,13 +124,8 @@ $(document).ready(function () {

                                                                  This is just a very simple vignette showing how to fit a degradation model for a parent compound with one transformation product using mkin. After loading the library we look a the data. We have observed concentrations in the column named value at the times specified in column time for the two observed variables named parent and m1.

                                                                  -
                                                                  library("mkin")
                                                                  -
                                                                  ## Loading required package: minpack.lm
                                                                  -
                                                                  ## Loading required package: rootSolve
                                                                  -
                                                                  ## Loading required package: inline
                                                                  -
                                                                  ## Loading required package: methods
                                                                  -
                                                                  ## Loading required package: parallel
                                                                  -
                                                                  print(FOCUS_2006_D)
                                                                  +
                                                                  library("mkin")
+print(FOCUS_2006_D)
                                                                  ##      name time  value
 ## 1  parent    0  99.46
 ## 2  parent    0 102.04
@@ -195,10 +190,10 @@ $(document).ready(function () {
 
                                                                  
 
                                                                  A comprehensive report of the results is obtained using the summary method for mkinfit objects.
                                                                  
 
                                                                  summary(fit)
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:48:50 2016 
-## Date of summary: Tue Jun 28 07:48:50 2016 
+## Date of fit:     Tue Jun 28 08:19:31 2016 
+## Date of summary: Tue Jun 28 08:19:31 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -206,7 +201,7 @@ $(document).ready(function () {
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 1.659 s
+## Fitted with method Port using 153 model solutions performed in 1.706 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 8435ce23..05b9bdbd 100644
--- a/vignettes/FOCUS_L.html
+++ b/vignettes/FOCUS_L.html
@@ -233,17 +233,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)
                                                                  
 
                                                                  Since mkin version 0.9-32 (July 2014), we can use shorthand notation like "SFO" for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.
                                                                  
 
                                                                  m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet = TRUE)
 summary(m.L1.SFO)
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:38:06 2016 
-## Date of summary: Tue Jun 28 07:38:06 2016 
+## Date of fit:     Tue Jun 28 08:19:32 2016 
+## Date of summary: Tue Jun 28 08:19:32 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.235 s
+## Fitted with method Port using 37 model solutions performed in 0.245 s
 ## 
 ## Weighting: none
 ## 
@@ -326,10 +326,10 @@ summary(m.L1.SFO)
                                                                  
 
                                                                  plot(m.L1.FOMC, show_errmin = TRUE, main = "FOCUS L1 - FOMC")
                                                                  
 
                                                                  
 
                                                                  summary(m.L1.FOMC, data = FALSE)
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:38:07 2016 
-## Date of summary: Tue Jun 28 07:38:07 2016 
+## Date of fit:     Tue Jun 28 08:19:34 2016 
+## Date of summary: Tue Jun 28 08:19:34 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -341,7 +341,7 @@ summary(m.L1.SFO)
                                                                  
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 1.119 s
+## Fitted with method Port using 188 model solutions performed in 1.216 s
 ## 
 ## Weighting: none
 ## 
@@ -423,17 +423,17 @@ plot(m.L2.FOMC, show_residuals = TRUE,
      main = "FOCUS L2 - FOMC")
                                                                  
 
                                                                  
 
                                                                  summary(m.L2.FOMC, data = FALSE)
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:38:09 2016 
-## Date of summary: Tue Jun 28 07:38:09 2016 
+## Date of fit:     Tue Jun 28 08:19:36 2016 
+## Date of summary: Tue Jun 28 08:19:36 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.492 s
+## Fitted with method Port using 81 model solutions performed in 0.537 s
 ## 
 ## Weighting: none
 ## 
@@ -493,10 +493,10 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
      main = "FOCUS L2 - DFOP")
                                                                  
 
                                                                  
 
                                                                  summary(m.L2.DFOP, data = FALSE)
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:38:11 2016 
-## Date of summary: Tue Jun 28 07:38:11 2016 
+## Date of fit:     Tue Jun 28 08:19:39 2016 
+## Date of summary: Tue Jun 28 08:19:39 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -505,7 +505,7 @@ plot(m.L2.DFOP, show_residuals = TRUE, show_errmin = TRUE,
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 2.04 s
+## Fitted with method Port using 336 model solutions performed in 2.267 s
 ## 
 ## Weighting: none
 ## 
@@ -582,10 +582,10 @@ plot(mm.L3)
                                                                  
 
                                                                  The objects returned by mmkin are arranged like a matrix, with models as a row index and datasets as a column index.
                                                                  
 
                                                                  We can extract the summary and plot for e.g. the DFOP fit, using square brackets for indexing which will result in the use of the summary and plot functions working on mkinfit objects.
                                                                  
 
                                                                  summary(mm.L3[["DFOP", 1]])
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:38:13 2016 
-## Date of summary: Tue Jun 28 07:38:13 2016 
+## Date of fit:     Tue Jun 28 08:19:41 2016 
+## Date of summary: Tue Jun 28 08:19:42 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -594,7 +594,7 @@ plot(mm.L3)
                                                                  
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.846 s
+## Fitted with method Port using 137 model solutions performed in 0.924 s
 ## 
 ## Weighting: none
 ## 
@@ -682,17 +682,17 @@ plot(mm.L4)
                                                                  
 
                                                                  
 
                                                                  The χ2 error level of 3.3% as well as the plot suggest that the SFO model fits very well. The error level at which the χ2 test passes is slightly lower for the FOMC model. However, the difference appears negligible.
                                                                  
 
                                                                  summary(mm.L4[["SFO", 1]], data = FALSE)
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:38:14 2016 
-## Date of summary: Tue Jun 28 07:38:14 2016 
+## Date of fit:     Tue Jun 28 08:19:42 2016 
+## Date of summary: Tue Jun 28 08:19:43 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.283 s
+## Fitted with method Port using 46 model solutions performed in 0.307 s
 ## 
 ## Weighting: none
 ## 
@@ -742,17 +742,17 @@ plot(mm.L4)
                                                                  
 ##        DT50 DT90
 ## parent  106  352
                                                                  
 
                                                                  summary(mm.L4[["FOMC", 1]], data = FALSE)
                                                                  
-
                                                                  ## mkin version:    0.9.43 
+
                                                                  ## mkin version:    0.9.43.9000 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 07:38:14 2016 
-## Date of summary: Tue Jun 28 07:38:15 2016 
+## Date of fit:     Tue Jun 28 08:19:43 2016 
+## Date of summary: Tue Jun 28 08:19:43 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.383 s
+## Fitted with method Port using 66 model solutions performed in 0.414 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index efda950f..1f9560b0 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index c3ffb035..cec76ef9 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -226,13 +226,8 @@ div.tocify {
 
                                                                  ##            gcc 
 ## "/usr/bin/gcc"
                                                                  
 
                                                                  First, we build a simple degradation model for a parent compound with one metabolite.
                                                                  
-
                                                                  library("mkin")
                                                                  
-
                                                                  ## Loading required package: minpack.lm
                                                                  
-
                                                                  ## Loading required package: rootSolve
                                                                  
-
                                                                  ## Loading required package: inline
                                                                  
-
                                                                  ## Loading required package: methods
                                                                  
-
                                                                  ## Loading required package: parallel
                                                                  
-
                                                                  SFO_SFO <- mkinmod(
+
                                                                  library("mkin")
+SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"))
                                                                  
 
                                                                  ## Successfully compiled differential equation model from auto-generated C code.
                                                                  
@@ -255,22 +250,22 @@ mb.1 <- microbenchmark(
 print(mb.1)
                                                                  
 
                                                                  ## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 13.694897 13.774112 13.820936 13.853327 13.883956
-##       Eigenvalue based  2.087861  2.089503  2.116323  2.091145  2.130555
-##      deSolve, compiled  1.794975  1.799892  1.814653  1.804808  1.824492
-##        max neval cld
-##  13.914585     3   c
-##   2.169964     3  b 
-##   1.844177     3 a
                                                                  
+##  deSolve, not compiled 25.422123 25.889685 26.065978 26.357247 26.387905
+##       Eigenvalue based  2.243667  2.254539  2.277770  2.265412  2.294821
+##      deSolve, compiled  1.849468  1.865343  1.871339  1.881219  1.882274
+##       max neval cld
+##  26.41856     3   b
+##   2.32423     3  a 
+##   1.88333     3  a
                                                                  
 
                                                                  autoplot(mb.1)
                                                                  
-
                                                                  
-
                                                                  We see that using the compiled model is by a factor of 7.7 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:
                                                                  
+
                                                                  
+
                                                                  We see that using the compiled model is by a factor of 14 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 7.675788
-## Eigenvalue based      1.158652
-## deSolve, compiled     1.000000
                                                                  
+
                                                                  ##                          median
+## deSolve, not compiled 14.010730
+## Eigenvalue based       1.204226
+## deSolve, compiled      1.000000

                                                                  Benchmark for a model that can not be solved with Eigenvalues

                                                                  @@ -290,20 +285,20 @@ smb.1["median"]/smb.1["deSolve, compiled", "median" 
                                                                  smb.2 <- summary(mb.2)
 print(mb.2)
                                                                  ## Unit: seconds
-##                   expr       min        lq      mean   median        uq
-##  deSolve, not compiled 29.120048 29.170013 29.246607 29.21998 29.309886
-##      deSolve, compiled  3.338458  3.343954  3.379437  3.34945  3.399926
+##                   expr       min       lq      mean    median        uq
+##  deSolve, not compiled 54.386189 54.39423 54.477986 54.402271 54.523884
+##      deSolve, compiled  3.424205  3.53522  3.574587  3.646236  3.649778
 ##        max neval cld
-##  29.399796     3   b
-##   3.450402     3  a
                                                                  +## 54.645498 3 b +## 3.653319 3 a 
                                                                  smb.2["median"]/smb.2["deSolve, compiled", "median"]
                                                                  ##   median
 ## 1     NA
 ## 2     NA
                                                                  autoplot(mb.2)
                                                                  -

                                                                  -

                                                                  Here we get a performance benefit of a factor of 8.7 using the version of the differential equation model compiled from C code!

                                                                  -

                                                                  This vignette was built with mkin 0.9.43 on

                                                                  +

                                                                  +

                                                                  Here we get a performance benefit of a factor of 14.9 using the version of the differential equation model compiled from C code!

                                                                  +

                                                                  This vignette was built with mkin 0.9.43.9000 on

                                                                  ## R version 3.3.1 (2016-06-21)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)
                                                                  diff --git a/vignettes/mkin.html b/vignettes/mkin.html index 54605dfc..f9704eda 100644 --- a/vignettes/mkin.html +++ b/vignettes/mkin.html @@ -236,14 +236,8 @@ div.tocify {

                                                                  Abstract

                                                                  In the regulatory evaluation of chemical substances like plant protection products (pesticides), biocides and other chemicals, degradation data play an important role. For the evaluation of pesticide degradation experiments, detailed guidance has been developed, based on nonlinear optimisation. The R add-on package mkin (Ranke 2016) implements fitting some of the models recommended in this guidance from within R and calculates some statistical measures for data series within one or more compartments, for parent and metabolites.

                                                                  -
                                                                  require(mkin)
                                                                  -
                                                                  ## Loading required package: mkin
                                                                  -
                                                                  ## Loading required package: minpack.lm
                                                                  -
                                                                  ## Loading required package: rootSolve
                                                                  -
                                                                  ## Loading required package: inline
                                                                  -
                                                                  ## Loading required package: methods
                                                                  -
                                                                  ## Loading required package: parallel
                                                                  -
                                                                  m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
+
                                                                  require(mkin)
+m_SFO_SFO_SFO <- mkinmod(parent = mkinsub("SFO", "M1"),
                          M1 = mkinsub("SFO", "M2"),
                          M2 = mkinsub("SFO"), 
                          use_of_ff = "max", quiet = TRUE)
-- 
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