From 3b399df5231576880fd9e0ae7253064d82edfe86 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 10 Sep 2016 04:03:08 +0200 Subject: Static documentation rebuilt by staticdocs::build_site() --- GNUmakefile | 4 +- inst/web/DFOP.solution.html | 4 +- inst/web/Extract.mmkin.html | 46 ++++++++++++---------- 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 | 33 +++++++++------- 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 | 10 ++--- 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 | 14 +++---- inst/web/vignettes/FOCUS_L.html | 63 ++++++++++++++++--------------- inst/web/vignettes/FOCUS_Z.pdf | Bin 238789 -> 238636 bytes inst/web/vignettes/compiled_models.html | 49 ++++++++++++------------ inst/web/vignettes/mkin.html | 14 ++++--- vignettes/FOCUS_D.html | 14 +++---- vignettes/FOCUS_L.html | 63 ++++++++++++++++--------------- vignettes/FOCUS_Z.pdf | Bin 238789 -> 238636 bytes vignettes/compiled_models.html | 49 ++++++++++++------------ vignettes/mkin.html | 14 ++++--- 49 files changed, 279 insertions(+), 260 deletions(-) diff --git a/GNUmakefile b/GNUmakefile index ad455ae5..062f4ead 100644 --- a/GNUmakefile +++ b/GNUmakefile @@ -87,9 +87,7 @@ vignettes/%.html: vignettes/mkin_vignettes.css vignettes/%.Rmd vignettes: vignettes/mkin.html vignettes/FOCUS_D.html vignettes/FOCUS_L.html vignettes/FOCUS_Z.pdf vignettes/compiled_models.html sd: - @echo Now execute - @echo "\n staticdocs::build_site()\n" - $(RBIN)/R + "$(RBIN)/Rscript" -e "staticdocs::build_site()" git add -A git commit -m 'Static documentation rebuilt by staticdocs::build_site()' -e diff --git a/inst/web/DFOP.solution.html b/inst/web/DFOP.solution.html index f6d32d70..e4460aec 100644 --- a/inst/web/DFOP.solution.html +++ b/inst/web/DFOP.solution.html @@ -2,7 +2,7 @@ -DFOP.solution. mkin 0.9.44 +DFOP.solution. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
- mkin 0.9.44 + mkin 0.9.44.9000
  • Index
    • diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 134bb4cb..e4225ffd 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -2,7 +2,7 @@ -[.mmkin. mkin 0.9.44 +[.mmkin. mkin 0.9.44.9000
    - mkin 0.9.44 + mkin 0.9.44.9000
    • Index
      • @@ -137,8 +137,10 @@ log_alpha -95.699832 6618.85833 -6352.46648 log_beta 93.176993 -6352.46648 6101.23483 $residuals - parent parent parent parent parent parent parent parent - 1.046192647 -3.322396479 3.655156669 -1.705316770 0.406306255 -0.123734689 -0.036886982 -0.006240458 + parent parent parent parent parent parent + 1.046192647 -3.322396479 3.655156669 -1.705316770 0.406306255 -0.123734689 + parent parent +-0.036886982 -0.006240458 $ms [1] 3.572863 @@ -181,7 +183,7 @@ $calls $time user system elapsed - 0.712 0.004 0.716 + 0.260 0.000 0.259 $mkinmod <mkinmod> model generated with @@ -367,7 +369,7 @@ function (P) } return(mC) } -<environment: 0x48ad868> +<environment: 0x37c6c70> $cost_notrans function (P) @@ -389,7 +391,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x48ad868> +<environment: 0x37c6c70> $hessian_notrans parent_0 alpha beta @@ -455,7 +457,7 @@ $bparms.state 99.66619 $date -[1] "Tue Jun 28 10:24:49 2016" +[1] "Sat Sep 10 04:12:07 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -496,8 +498,10 @@ parent_0 4.163631 -94.09343 log_k_parent_sink -94.093431 6311.34610 $residuals - parent parent parent parent parent parent parent parent - 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730 -0.24260405 -0.07020339 + parent parent parent parent parent parent + 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730 + parent parent +-0.24260405 -0.07020339 $ms [1] 3.831956 @@ -540,7 +544,7 @@ $calls $time user system elapsed - 0.204 0.000 0.205 + 0.068 0.000 0.069 $mkinmod <mkinmod> model generated with @@ -727,7 +731,7 @@ function (P) } return(mC) } -<environment: 0x561e810> +<environment: 0x4cb0ed0> $cost_notrans function (P) @@ -749,7 +753,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x561e810> +<environment: 0x4cb0ed0> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +816,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 10:24:48 2016" +[1] "Sat Sep 10 04:12:07 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -846,8 +850,10 @@ parent_0 4.163631 -94.09343 log_k_parent_sink -94.093431 6311.34610 $residuals - parent parent parent parent parent parent parent parent - 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730 -0.24260405 -0.07020339 + parent parent parent parent parent parent + 0.55407218 -2.98452128 4.20445742 -1.68599939 -0.58185357 -0.72033730 + parent parent +-0.24260405 -0.07020339 $ms [1] 3.831956 @@ -890,7 +896,7 @@ $calls $time user system elapsed - 0.204 0.000 0.205 + 0.068 0.000 0.069 $mkinmod <mkinmod> model generated with @@ -1077,7 +1083,7 @@ function (P) } return(mC) } -<environment: 0x561e810> +<environment: 0x4cb0ed0> $cost_notrans function (P) @@ -1099,7 +1105,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x561e810> +<environment: 0x4cb0ed0> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1168,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 10:24:48 2016" +[1] "Sat Sep 10 04:12:07 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 2a4de917..a7a17ea3 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 0.9.44 +FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
      - mkin 0.9.44 + mkin 0.9.44.9000
      • 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 f5860202..143a6418 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 0.9.44 +FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
        - mkin 0.9.44 + mkin 0.9.44.9000
        • 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 4894a54a..7dfa321f 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 0.9.44 +FOCUS_2006_HS_ref_A_to_F. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
          - mkin 0.9.44 + mkin 0.9.44.9000
          • 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 45012d12..841f9932 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 0.9.44 +FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
            - mkin 0.9.44 + mkin 0.9.44.9000
            • Index
              • diff --git a/inst/web/FOCUS_2006_datasets.html b/inst/web/FOCUS_2006_datasets.html index abb38738..7d561201 100644 --- a/inst/web/FOCUS_2006_datasets.html +++ b/inst/web/FOCUS_2006_datasets.html @@ -2,7 +2,7 @@ -FOCUS_2006_datasets. mkin 0.9.44 +FOCUS_2006_datasets. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
              - mkin 0.9.44 + mkin 0.9.44.9000
              • Index
                • diff --git a/inst/web/FOMC.solution.html b/inst/web/FOMC.solution.html index a8a80911..3c01aee0 100644 --- a/inst/web/FOMC.solution.html +++ b/inst/web/FOMC.solution.html @@ -2,7 +2,7 @@ -FOMC.solution. mkin 0.9.44 +FOMC.solution. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                - mkin 0.9.44 + mkin 0.9.44.9000
                • Index
                  • diff --git a/inst/web/HS.solution.html b/inst/web/HS.solution.html index 0ed5779f..fb60b266 100644 --- a/inst/web/HS.solution.html +++ b/inst/web/HS.solution.html @@ -2,7 +2,7 @@ -HS.solution. mkin 0.9.44 +HS.solution. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                  - mkin 0.9.44 + mkin 0.9.44.9000
                  • Index
                    • diff --git a/inst/web/IORE.solution.html b/inst/web/IORE.solution.html index 45f01ac1..dce131a7 100644 --- a/inst/web/IORE.solution.html +++ b/inst/web/IORE.solution.html @@ -2,7 +2,7 @@ -IORE.solution. mkin 0.9.44 +IORE.solution. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                    - mkin 0.9.44 + mkin 0.9.44.9000
                    • Index
                      • diff --git a/inst/web/SFO.solution.html b/inst/web/SFO.solution.html index c740a6e5..de8b2f37 100644 --- a/inst/web/SFO.solution.html +++ b/inst/web/SFO.solution.html @@ -2,7 +2,7 @@ -SFO.solution. mkin 0.9.44 +SFO.solution. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                      - mkin 0.9.44 + mkin 0.9.44.9000
                      • Index
                        • diff --git a/inst/web/SFORB.solution.html b/inst/web/SFORB.solution.html index 10de4783..0a18a799 100644 --- a/inst/web/SFORB.solution.html +++ b/inst/web/SFORB.solution.html @@ -2,7 +2,7 @@ -SFORB.solution. mkin 0.9.44 +SFORB.solution. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                        - mkin 0.9.44 + mkin 0.9.44.9000
                        • Index
                          • diff --git a/inst/web/add_err.html b/inst/web/add_err.html index 1ab38bb8..c1f2f42f 100644 --- a/inst/web/add_err.html +++ b/inst/web/add_err.html @@ -2,7 +2,7 @@ -add_err. mkin 0.9.44 +add_err. mkin 0.9.44.9000
                          - mkin 0.9.44 + mkin 0.9.44.9000
                          • Index
                            • diff --git a/inst/web/endpoints.html b/inst/web/endpoints.html index 4835f156..e72b5a08 100644 --- a/inst/web/endpoints.html +++ b/inst/web/endpoints.html @@ -2,7 +2,7 @@ -endpoints. mkin 0.9.44 +endpoints. mkin 0.9.44.9000
                            - mkin 0.9.44 + mkin 0.9.44.9000
                            • Index
                              • diff --git a/inst/web/geometric_mean.html b/inst/web/geometric_mean.html index ec6c3704..1bccba14 100644 --- a/inst/web/geometric_mean.html +++ b/inst/web/geometric_mean.html @@ -2,7 +2,7 @@ -geometric_mean. mkin 0.9.44 +geometric_mean. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                              - mkin 0.9.44 + mkin 0.9.44.9000
                              • Index
                                • diff --git a/inst/web/ilr.html b/inst/web/ilr.html index baa5ed74..7e37a15f 100644 --- a/inst/web/ilr.html +++ b/inst/web/ilr.html @@ -2,7 +2,7 @@ -ilr. mkin 0.9.44 +ilr. mkin 0.9.44.9000
                                - mkin 0.9.44 + mkin 0.9.44.9000
                                • Index
                                  • diff --git a/inst/web/index.html b/inst/web/index.html index 22afd22e..a78e5877 100644 --- a/inst/web/index.html +++ b/inst/web/index.html @@ -2,7 +2,7 @@ -Index. mkin 0.9.44 +Index. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                                  - mkin 0.9.44 + mkin 0.9.44.9000
                                  • Index
                                    • diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 09609b0c..9972571a 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -2,7 +2,7 @@ -mccall81_245T. mkin 0.9.44 +mccall81_245T. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                                    - mkin 0.9.44 + mkin 0.9.44.9000
                                    • Index
                                      • @@ -112,19 +112,20 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
                                    -
                                    mkin version: 0.9.44 +
                                    mkin version: 0.9.44.9000 R version: 3.3.1 -Date of fit: Tue Jun 28 10:25:07 2016 -Date of summary: Tue Jun 28 10:25:08 2016 +Date of fit: Sat Sep 10 04:12:13 2016 +Date of summary: Sat Sep 10 04:12:13 2016 Equations: d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 -d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol - k_phenol_anisole * phenol +d_phenol = + k_T245_phenol * T245 - k_phenol_sink * phenol - + k_phenol_anisole * phenol 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 3.86 s +Fitted with method Port using 246 model solutions performed in 1.456 s Weighting: none @@ -159,12 +160,18 @@ log_k_phenol_anisole -0.9037 0.30580 -1.544 -0.2637 log_k_anisole_sink -5.0090 0.11180 -5.243 -4.7750 Parameter correlation: - T245_0 log_k_T245_sink log_k_T245_phenol log_k_phenol_anisole log_k_anisole_sink -T245_0 1.00000 0.63761 -0.1742 -0.05948 -0.1621 -log_k_T245_sink 0.63761 1.00000 -0.3831 0.08745 -0.6047 -log_k_T245_phenol -0.17416 -0.38313 1.0000 -0.30470 0.5227 -log_k_phenol_anisole -0.05948 0.08745 -0.3047 1.00000 -0.1774 -log_k_anisole_sink -0.16208 -0.60469 0.5227 -0.17744 1.0000 + T245_0 log_k_T245_sink log_k_T245_phenol +T245_0 1.00000 0.63761 -0.1742 +log_k_T245_sink 0.63761 1.00000 -0.3831 +log_k_T245_phenol -0.17416 -0.38313 1.0000 +log_k_phenol_anisole -0.05948 0.08745 -0.3047 +log_k_anisole_sink -0.16208 -0.60469 0.5227 + log_k_phenol_anisole log_k_anisole_sink +T245_0 -0.05948 -0.1621 +log_k_T245_sink 0.08745 -0.6047 +log_k_T245_phenol -0.30470 0.5227 +log_k_phenol_anisole 1.00000 -0.1774 +log_k_anisole_sink -0.17744 1.0000 Residual standard error: 2.706 on 19 degrees of freedom diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index 7109f1c9..68335f27 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 0.9.44 +mkin_long_to_wide. mkin 0.9.44.9000
                                    - mkin 0.9.44 + mkin 0.9.44.9000
                                    • Index
                                      • diff --git a/inst/web/mkin_wide_to_long.html b/inst/web/mkin_wide_to_long.html index d783d5a2..26e95176 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 0.9.44 +mkin_wide_to_long. mkin 0.9.44.9000
                                      - mkin 0.9.44 + mkin 0.9.44.9000
                                      • Index
                                        • diff --git a/inst/web/mkinds.html b/inst/web/mkinds.html index 6021dd89..ffb7e781 100644 --- a/inst/web/mkinds.html +++ b/inst/web/mkinds.html @@ -2,7 +2,7 @@ -mkinds. mkin 0.9.44 +mkinds. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                                        - mkin 0.9.44 + mkin 0.9.44.9000
                                        • Index
                                          • diff --git a/inst/web/mkinerrmin.html b/inst/web/mkinerrmin.html index 5cab6f43..25179d52 100644 --- a/inst/web/mkinerrmin.html +++ b/inst/web/mkinerrmin.html @@ -2,7 +2,7 @@ -mkinerrmin. mkin 0.9.44 +mkinerrmin. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                                          - mkin 0.9.44 + mkin 0.9.44.9000
                                          • Index
                                            • diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 89b22754..910a43ec 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -2,7 +2,7 @@ -mkinfit. mkin 0.9.44 +mkinfit. mkin 0.9.44.9000
                                            - mkin 0.9.44 + mkin 0.9.44.9000
                                            • Index
                                              • @@ -323,17 +323,17 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
                                            -
                                            mkin version: 0.9.44 +
                                            mkin version: 0.9.44.9000 R version: 3.3.1 -Date of fit: Tue Jun 28 10:25:14 2016 -Date of summary: Tue Jun 28 10:25:14 2016 +Date of fit: Sat Sep 10 04:12:15 2016 +Date of summary: Sat Sep 10 04:12:15 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 0.44 s +Fitted with method Port using 64 model solutions performed in 0.156 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 - 2.852 2.240 2.272 + 1.228 1.216 0.923
                                            coef(fit)
                                            diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index 04b4a453..7e57f022 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9.44 +mkinmod. mkin 0.9.44.9000
                                            - mkin 0.9.44 + mkin 0.9.44.9000
                                            • Index
                                              • diff --git a/inst/web/mkinparplot.html b/inst/web/mkinparplot.html index 45eb9850..48a795d6 100644 --- a/inst/web/mkinparplot.html +++ b/inst/web/mkinparplot.html @@ -2,7 +2,7 @@ -mkinparplot. mkin 0.9.44 +mkinparplot. mkin 0.9.44.9000
                                              - mkin 0.9.44 + mkin 0.9.44.9000
                                              • Index
                                                • diff --git a/inst/web/mkinplot.html b/inst/web/mkinplot.html index b84b62f9..cd267e3f 100644 --- a/inst/web/mkinplot.html +++ b/inst/web/mkinplot.html @@ -2,7 +2,7 @@ -mkinplot. mkin 0.9.44 +mkinplot. mkin 0.9.44.9000
                                                - mkin 0.9.44 + mkin 0.9.44.9000
                                                • Index
                                                  • diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index 728c4e10..fbf06007 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -2,7 +2,7 @@ -mkinpredict. mkin 0.9.44 +mkinpredict. mkin 0.9.44.9000
                                                  - mkin 0.9.44 + mkin 0.9.44.9000
                                                  • Index
                                                    • @@ -304,7 +304,7 @@ 201 20 4.978707 27.46227
                                                  user system elapsed - 0.032 0.040 0.011 + 0.024 0.004 0.005
                                                  system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -315,7 +315,7 @@ 201 20 4.978707 27.46227
                                                  user system elapsed - 0.000 0.020 0.005 + 0.000 0.020 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 - 0.140 0.000 0.139 + 0.036 0.000 0.036
                                                  diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index 49769d62..6fa9423c 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9.44 +mkinresplot. mkin 0.9.44.9000
                                                  - mkin 0.9.44 + mkin 0.9.44.9000
                                                  • Index
                                                    • diff --git a/inst/web/mkinsub.html b/inst/web/mkinsub.html index 6fbd12f8..597dbc8c 100644 --- a/inst/web/mkinsub.html +++ b/inst/web/mkinsub.html @@ -2,7 +2,7 @@ -mkinsub. mkin 0.9.44 +mkinsub. mkin 0.9.44.9000
                                                    - mkin 0.9.44 + mkin 0.9.44.9000
                                                    • Index
                                                      • diff --git a/inst/web/mmkin.html b/inst/web/mmkin.html index a8a5499b..765b1dd6 100644 --- a/inst/web/mmkin.html +++ b/inst/web/mmkin.html @@ -2,7 +2,7 @@ -mmkin. mkin 0.9.44 +mmkin. mkin 0.9.44.9000
                                                      - mkin 0.9.44 + mkin 0.9.44.9000
                                                      • Index
                                                        • diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html index 938963af..d253de45 100644 --- a/inst/web/plot.mkinfit.html +++ b/inst/web/plot.mkinfit.html @@ -2,7 +2,7 @@ -plot.mkinfit. mkin 0.9.44 +plot.mkinfit. mkin 0.9.44.9000
                                                        - mkin 0.9.44 + mkin 0.9.44.9000
                                                        • Index
                                                          • diff --git a/inst/web/plot.mmkin.html b/inst/web/plot.mmkin.html index 070892b0..e7d1fbcf 100644 --- a/inst/web/plot.mmkin.html +++ b/inst/web/plot.mmkin.html @@ -2,7 +2,7 @@ -plot.mmkin. mkin 0.9.44 +plot.mmkin. mkin 0.9.44.9000
                                                          - mkin 0.9.44 + mkin 0.9.44.9000
                                                          • Index
                                                            • diff --git a/inst/web/print.mkinds.html b/inst/web/print.mkinds.html index f582702b..2842bf4f 100644 --- a/inst/web/print.mkinds.html +++ b/inst/web/print.mkinds.html @@ -2,7 +2,7 @@ -print.mkinds. mkin 0.9.44 +print.mkinds. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                                                            - mkin 0.9.44 + mkin 0.9.44.9000
                                                            • Index
                                                              • diff --git a/inst/web/print.mkinmod.html b/inst/web/print.mkinmod.html index 7e0d8140..a2440f3b 100644 --- a/inst/web/print.mkinmod.html +++ b/inst/web/print.mkinmod.html @@ -2,7 +2,7 @@ -print.mkinmod. mkin 0.9.44 +print.mkinmod. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                                                              - mkin 0.9.44 + mkin 0.9.44.9000
                                                              • Index
                                                                • diff --git a/inst/web/schaefer07_complex_case.html b/inst/web/schaefer07_complex_case.html index 387dac46..b6d0528a 100644 --- a/inst/web/schaefer07_complex_case.html +++ b/inst/web/schaefer07_complex_case.html @@ -2,7 +2,7 @@ -schaefer07_complex_case. mkin 0.9.44 +schaefer07_complex_case. mkin 0.9.44.9000 @@ -32,7 +32,7 @@
                                                                - mkin 0.9.44 + mkin 0.9.44.9000
                                                                • Index
                                                                  • diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index dfa939ae..936350df 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -2,7 +2,7 @@ -summary.mkinfit. mkin 0.9.44 +summary.mkinfit. mkin 0.9.44.9000
                                                                  - mkin 0.9.44 + mkin 0.9.44.9000
                                                                  • Index
                                                                    • @@ -157,17 +157,17 @@

                                                                    Examples

                                                                      summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
 
                                                                    
-
                                                                    mkin version:    0.9.44 
+
                                                                    mkin version:    0.9.44.9000 
 R version:       3.3.1 
-Date of fit:     Tue Jun 28 10:25:34 2016 
-Date of summary: Tue Jun 28 10:25:34 2016 
+Date of fit:     Sat Sep 10 04:12:23 2016 
+Date of summary: Sat Sep 10 04:12:23 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 35 model solutions performed in 0.286 s
+Fitted with method Port using 35 model solutions performed in 0.078 s
 
 Weighting: none
 
diff --git a/inst/web/synthetic_data_for_UBA.html b/inst/web/synthetic_data_for_UBA.html
index 0d0326a5..0320a848 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 0.9.44
+synthetic_data_for_UBA_2014. mkin 0.9.44.9000
 
 
 
@@ -32,7 +32,7 @@
     
                                                                    
   
                                                                    
     
                                                                    
-      mkin 0.9.44
+      mkin 0.9.44.9000
       
                                                                    
         
                                                                      
           
                                                                    •  Index
                                                                      • 
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index b1207f6a..43c6cdc2 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -2,7 +2,7 @@
 
   
     
-transform_odeparms. mkin 0.9.44
+transform_odeparms. mkin 0.9.44.9000
 
 
   
                                                                      
     
                                                                      
-      mkin 0.9.44
+      mkin 0.9.44.9000
       
                                                                      
         
                                                                        
           
                                                                      •  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:    0.9.44 
+
                                                                      mkin version:    0.9.44.9000 
 R version:       3.3.1 
-Date of fit:     Tue Jun 28 10:25:37 2016 
-Date of summary: Tue Jun 28 10:25:37 2016 
+Date of fit:     Sat Sep 10 04:12:24 2016 
+Date of summary: Sat Sep 10 04:12:24 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 1.788 s
+Fitted with method Port using 153 model solutions performed in 0.682 s
 
 Weighting: none
 
diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html
index d60d1c7f..d02b1b61 100644
--- a/inst/web/vignettes/FOCUS_D.html
+++ b/inst/web/vignettes/FOCUS_D.html
@@ -11,7 +11,7 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Example Dataset D
 
@@ -24,7 +24,7 @@
 
 
 
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