From 7875935fdfc3c55e0ef328b3c3a4512a30011df1 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Wed, 23 Mar 2016 17:03:09 +0100 Subject: Added 'from_max_mean' to 'mkinfit'. - Now it is easier to do decline kinetics from the maximum occurrence - Static documentation rebuilt by staticdocs::build_site() - Fixed an URL in the README, thanks to the win-builder check with R-devel --- inst/web/DFOP.solution.html | 4 +-- inst/web/Extract.mmkin.html | 34 +++++++++--------- inst/web/FOCUS_2006_DFOP_ref_A_to_B.html | 4 +-- inst/web/FOCUS_2006_FOMC_ref_A_to_F.html | 4 +-- inst/web/FOCUS_2006_HS_ref_A_to_F.html | 4 +-- inst/web/FOCUS_2006_SFO_ref_A_to_F.html | 4 +-- inst/web/FOCUS_2006_datasets.html | 4 +-- inst/web/FOMC.solution.html | 4 +-- inst/web/HS.solution.html | 4 +-- inst/web/IORE.solution.html | 4 +-- inst/web/SFO.solution.html | 4 +-- inst/web/SFORB.solution.html | 4 +-- inst/web/endpoints.html | 4 +-- inst/web/geometric_mean.html | 4 +-- inst/web/ilr.html | 4 +-- inst/web/index.html | 4 +-- inst/web/mccall81_245T.html | 14 ++++---- inst/web/mkin_long_to_wide.html | 4 +-- inst/web/mkin_wide_to_long.html | 4 +-- inst/web/mkinds.html | 4 +-- inst/web/mkinerrmin.html | 4 +-- inst/web/mkinfit.html | 26 +++++++++----- 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 | 14 ++++---- inst/web/synthetic_data_for_UBA.html | 4 +-- inst/web/transform_odeparms.html | 14 ++++---- inst/web/vignettes/FOCUS_D.html | 18 +++++----- inst/web/vignettes/FOCUS_L.html | 20 +++++------ inst/web/vignettes/FOCUS_Z.pdf | Bin 224828 -> 225028 bytes inst/web/vignettes/compiled_models.html | 58 +++++++++++++++---------------- inst/web/vignettes/mkin.pdf | Bin 160263 -> 160263 bytes 42 files changed, 170 insertions(+), 162 deletions(-) (limited to 'inst') diff --git a/inst/web/DFOP.solution.html b/inst/web/DFOP.solution.html index b5bdbc33..fb73ffb8 100644 --- a/inst/web/DFOP.solution.html +++ b/inst/web/DFOP.solution.html @@ -2,7 +2,7 @@ -DFOP.solution. mkin 0.9.41.9000 +DFOP.solution. mkin 0.9.42 @@ -32,7 +32,7 @@
- mkin 0.9.41.9000 + mkin 0.9.42
  • Index
    • diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 3015a6c8..68cfaf9a 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -2,7 +2,7 @@ -[.mmkin. mkin 0.9.41.9000 +[.mmkin. mkin 0.9.42
    - mkin 0.9.41.9000 + mkin 0.9.42
    • Index
      • @@ -181,14 +181,14 @@ $calls $time user system elapsed - 0.264 0.000 0.262 + 0.280 0.000 0.279 $mkinmod <mkinmod> model generated with Use of formation fractions $use_of_ff: min Specification $spec: $parent -$type: FOMC +$type: FOMC; $sink: TRUE $observed name time value @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x4376e58> +<environment: 0x2d2bae8> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x4376e58> +<environment: 0x2d2bae8> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Wed Dec 9 10:16:48 2015" +[1] "Wed Mar 23 16:59:33 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -540,14 +540,14 @@ $calls $time user system elapsed - 0.084 0.004 0.086 + 0.096 0.004 0.102 $mkinmod <mkinmod> model generated with Use of formation fractions $use_of_ff: min Specification $spec: $parent -$type: SFO +$type: SFO; $sink: TRUE Coefficient matrix $coefmat available $observed @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x404d8f8> +<environment: 0x4975b58> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x404d8f8> +<environment: 0x4975b58> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Wed Dec 9 10:16:47 2015" +[1] "Wed Mar 23 16:59:32 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -890,14 +890,14 @@ $calls $time user system elapsed - 0.084 0.004 0.086 + 0.096 0.004 0.102 $mkinmod <mkinmod> model generated with Use of formation fractions $use_of_ff: min Specification $spec: $parent -$type: SFO +$type: SFO; $sink: TRUE Coefficient matrix $coefmat available $observed @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x404d8f8> +<environment: 0x4975b58> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x404d8f8> +<environment: 0x4975b58> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Wed Dec 9 10:16:47 2015" +[1] "Wed Mar 23 16:59:32 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 b009f6e6..76911ba7 100644 --- a/inst/web/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/inst/web/FOCUS_2006_DFOP_ref_A_to_B.html @@ -2,7 +2,7 @@ -FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.41.9000 +FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.42 @@ -32,7 +32,7 @@
      - mkin 0.9.41.9000 + mkin 0.9.42
      • 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 c28cd888..ac250110 100644 --- a/inst/web/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/inst/web/FOCUS_2006_FOMC_ref_A_to_F.html @@ -2,7 +2,7 @@ -FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.41.9000 +FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.42 @@ -32,7 +32,7 @@
        - mkin 0.9.41.9000 + mkin 0.9.42
        • 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 ad779e12..e7f5cdd5 100644 --- a/inst/web/FOCUS_2006_HS_ref_A_to_F.html +++ b/inst/web/FOCUS_2006_HS_ref_A_to_F.html @@ -2,7 +2,7 @@ -FOCUS_2006_HS_ref_A_to_F. mkin 0.9.41.9000 +FOCUS_2006_HS_ref_A_to_F. mkin 0.9.42 @@ -32,7 +32,7 @@
          - mkin 0.9.41.9000 + mkin 0.9.42
          • 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 391aa699..5bbdaa24 100644 --- a/inst/web/FOCUS_2006_SFO_ref_A_to_F.html +++ b/inst/web/FOCUS_2006_SFO_ref_A_to_F.html @@ -2,7 +2,7 @@ -FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.41.9000 +FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.42 @@ -32,7 +32,7 @@
            - mkin 0.9.41.9000 + mkin 0.9.42
            • Index
              • diff --git a/inst/web/FOCUS_2006_datasets.html b/inst/web/FOCUS_2006_datasets.html index 64ae3bd7..a2ea626c 100644 --- a/inst/web/FOCUS_2006_datasets.html +++ b/inst/web/FOCUS_2006_datasets.html @@ -2,7 +2,7 @@ -FOCUS_2006_datasets. mkin 0.9.41.9000 +FOCUS_2006_datasets. mkin 0.9.42 @@ -32,7 +32,7 @@
              - mkin 0.9.41.9000 + mkin 0.9.42
              • Index
                • diff --git a/inst/web/FOMC.solution.html b/inst/web/FOMC.solution.html index 06d2d233..2f6a4097 100644 --- a/inst/web/FOMC.solution.html +++ b/inst/web/FOMC.solution.html @@ -2,7 +2,7 @@ -FOMC.solution. mkin 0.9.41.9000 +FOMC.solution. mkin 0.9.42 @@ -32,7 +32,7 @@
                - mkin 0.9.41.9000 + mkin 0.9.42
                • Index
                  • diff --git a/inst/web/HS.solution.html b/inst/web/HS.solution.html index b7573295..d009aa98 100644 --- a/inst/web/HS.solution.html +++ b/inst/web/HS.solution.html @@ -2,7 +2,7 @@ -HS.solution. mkin 0.9.41.9000 +HS.solution. mkin 0.9.42 @@ -32,7 +32,7 @@
                  - mkin 0.9.41.9000 + mkin 0.9.42
                  • Index
                    • diff --git a/inst/web/IORE.solution.html b/inst/web/IORE.solution.html index b2b60111..1491bccb 100644 --- a/inst/web/IORE.solution.html +++ b/inst/web/IORE.solution.html @@ -2,7 +2,7 @@ -IORE.solution. mkin 0.9.41.9000 +IORE.solution. mkin 0.9.42 @@ -32,7 +32,7 @@
                    - mkin 0.9.41.9000 + mkin 0.9.42
                    • Index
                      • diff --git a/inst/web/SFO.solution.html b/inst/web/SFO.solution.html index a30000d8..33ba8778 100644 --- a/inst/web/SFO.solution.html +++ b/inst/web/SFO.solution.html @@ -2,7 +2,7 @@ -SFO.solution. mkin 0.9.41.9000 +SFO.solution. mkin 0.9.42 @@ -32,7 +32,7 @@
                      - mkin 0.9.41.9000 + mkin 0.9.42
                      • Index
                        • diff --git a/inst/web/SFORB.solution.html b/inst/web/SFORB.solution.html index 42c6baa9..42c5a57f 100644 --- a/inst/web/SFORB.solution.html +++ b/inst/web/SFORB.solution.html @@ -2,7 +2,7 @@ -SFORB.solution. mkin 0.9.41.9000 +SFORB.solution. mkin 0.9.42 @@ -32,7 +32,7 @@
                        - mkin 0.9.41.9000 + mkin 0.9.42
                        • Index
                          • diff --git a/inst/web/endpoints.html b/inst/web/endpoints.html index 8c9b557f..9ddcc8b4 100644 --- a/inst/web/endpoints.html +++ b/inst/web/endpoints.html @@ -2,7 +2,7 @@ -endpoints. mkin 0.9.41.9000 +endpoints. mkin 0.9.42
                          - mkin 0.9.41.9000 + mkin 0.9.42
                          • Index
                            • diff --git a/inst/web/geometric_mean.html b/inst/web/geometric_mean.html index 2323a337..9d47ebdc 100644 --- a/inst/web/geometric_mean.html +++ b/inst/web/geometric_mean.html @@ -2,7 +2,7 @@ -geometric_mean. mkin 0.9.41.9000 +geometric_mean. mkin 0.9.42 @@ -32,7 +32,7 @@
                            - mkin 0.9.41.9000 + mkin 0.9.42
                            • Index
                              • diff --git a/inst/web/ilr.html b/inst/web/ilr.html index b75c111f..cb0eef23 100644 --- a/inst/web/ilr.html +++ b/inst/web/ilr.html @@ -2,7 +2,7 @@ -ilr. mkin 0.9.41.9000 +ilr. mkin 0.9.42
                              - mkin 0.9.41.9000 + mkin 0.9.42
                              • Index
                                • diff --git a/inst/web/index.html b/inst/web/index.html index 17c5ba6e..09310304 100644 --- a/inst/web/index.html +++ b/inst/web/index.html @@ -2,7 +2,7 @@ -Index. mkin 0.9.41.9000 +Index. mkin 0.9.42 @@ -32,7 +32,7 @@
                                - mkin 0.9.41.9000 + mkin 0.9.42
                                • Index
                                  • diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index ef7753f1..598f4d76 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -2,7 +2,7 @@ -mccall81_245T. mkin 0.9.41.9000 +mccall81_245T. mkin 0.9.42 @@ -32,7 +32,7 @@
                                  - mkin 0.9.41.9000 + mkin 0.9.42
                                  • Index
                                    • @@ -112,10 +112,10 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
                                  -
                                  mkin version: 0.9.41.9000 -R version: 3.2.2 -Date of fit: Wed Dec 9 10:16:55 2015 -Date of summary: Wed Dec 9 10:16:55 2015 +
                                  mkin version: 0.9.42 +R version: 3.2.4 +Date of fit: Wed Mar 23 16:59:40 2016 +Date of summary: Wed Mar 23 16:59:40 2016 Equations: d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -124,7 +124,7 @@ d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole Model predictions using solution type deSolve -Fitted with method Port using 246 model solutions performed in 1.383 s +Fitted with method Port using 246 model solutions performed in 1.469 s Weighting: none diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index 3bb32a4d..de36532f 100644 --- a/inst/web/mkin_long_to_wide.html +++ b/inst/web/mkin_long_to_wide.html @@ -2,7 +2,7 @@ -mkin_long_to_wide. mkin 0.9.41.9000 +mkin_long_to_wide. mkin 0.9.42
                                  - mkin 0.9.41.9000 + mkin 0.9.42
                                  • Index
                                    • diff --git a/inst/web/mkin_wide_to_long.html b/inst/web/mkin_wide_to_long.html index 82dba968..08abc942 100644 --- a/inst/web/mkin_wide_to_long.html +++ b/inst/web/mkin_wide_to_long.html @@ -2,7 +2,7 @@ -mkin_wide_to_long. mkin 0.9.41.9000 +mkin_wide_to_long. mkin 0.9.42
                                    - mkin 0.9.41.9000 + mkin 0.9.42
                                    • Index
                                      • diff --git a/inst/web/mkinds.html b/inst/web/mkinds.html index d883c8e0..5e0f5001 100644 --- a/inst/web/mkinds.html +++ b/inst/web/mkinds.html @@ -2,7 +2,7 @@ -mkinds. mkin 0.9.41.9000 +mkinds. mkin 0.9.42 @@ -32,7 +32,7 @@
                                      - mkin 0.9.41.9000 + mkin 0.9.42
                                      • Index
                                        • diff --git a/inst/web/mkinerrmin.html b/inst/web/mkinerrmin.html index 0aafc760..f5ab043f 100644 --- a/inst/web/mkinerrmin.html +++ b/inst/web/mkinerrmin.html @@ -2,7 +2,7 @@ -mkinerrmin. mkin 0.9.41.9000 +mkinerrmin. mkin 0.9.42 @@ -32,7 +32,7 @@
                                        - mkin 0.9.41.9000 + mkin 0.9.42
                                        • Index
                                          • diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 3c48dcc0..75d8be8b 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -2,7 +2,7 @@ -mkinfit. mkin 0.9.41.9000 +mkinfit. mkin 0.9.42
                                          - mkin 0.9.41.9000 + mkin 0.9.42
                                          • Index
                                            • @@ -56,7 +56,7 @@

                                            Usage

                                            - 
                                            mkinfit(mkinmod, observed,  parms.ini = "auto", state.ini = "auto", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1],  solution_type = c("auto", "analytical", "eigen", "deSolve"), method.ode = "lsoda", use_compiled = "auto", method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"), maxit.modFit = "auto", control.modFit = list(), transform_rates = TRUE, transform_fractions = TRUE, plot = FALSE, quiet = FALSE, err = NULL, weight = "none",  scaleVar = FALSE,  atol = 1e-8, rtol = 1e-10, n.outtimes = 100,  reweight.method = NULL, reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...)
                                            + 
                                            mkinfit(mkinmod, observed,  parms.ini = "auto", state.ini = "auto", fixed_parms = NULL, fixed_initials = names(mkinmod$diffs)[-1],  from_max_mean = FALSE, solution_type = c("auto", "analytical", "eigen", "deSolve"), method.ode = "lsoda", use_compiled = "auto", method.modFit = c("Port", "Marq", "SANN", "Nelder-Mead", "BFGS", "CG", "L-BFGS-B"), maxit.modFit = "auto", control.modFit = list(), transform_rates = TRUE, transform_fractions = TRUE, plot = FALSE, quiet = FALSE, err = NULL, weight = "none",  scaleVar = FALSE,  atol = 1e-8, rtol = 1e-10, n.outtimes = 100,  reweight.method = NULL, reweight.tol = 1e-8, reweight.max.iter = 10, trace_parms = FALSE, ...)

                                            Arguments

                                            @@ -113,6 +113,14 @@ The names of model variables for which the initial state at time 0 should be excluded from the optimisation. Defaults to all state variables except for the first one. + +
                                            from_max_mean
                                            +
                                            + If this is set to TRUE, and the model has only one observed variable, then + data before the time of the maximum observed value (after averaging for each + sampling time) are discarded, and this time is subtracted from all + remaining time values, so the time of the maximum observed mean value is + the new time zero.
                                            solution_type
                                            @@ -315,17 +323,17 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
                                            -
                                            mkin version: 0.9.41.9000 -R version: 3.2.2 -Date of fit: Wed Dec 9 10:16:57 2015 -Date of summary: Wed Dec 9 10:16:57 2015 +
                                            mkin version: 0.9.42 +R version: 3.2.4 +Date of fit: Wed Mar 23 16:59:43 2016 +Date of summary: Wed Mar 23 16:59:43 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 0.189 s +Fitted with method Port using 64 model solutions performed in 0.195 s Weighting: none @@ -401,7 +409,7 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))
                                            user system elapsed - 1.184 1.180 0.891 + 1.200 1.272 0.936
                                            coef(fit)
                                            diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index ea549f29..b3a396b9 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9.41.9000 +mkinmod. mkin 0.9.42
                                            - mkin 0.9.41.9000 + mkin 0.9.42
                                            • Index
                                              • diff --git a/inst/web/mkinparplot.html b/inst/web/mkinparplot.html index 8027af58..8eee6868 100644 --- a/inst/web/mkinparplot.html +++ b/inst/web/mkinparplot.html @@ -2,7 +2,7 @@ -mkinparplot. mkin 0.9.41.9000 +mkinparplot. mkin 0.9.42
                                              - mkin 0.9.41.9000 + mkin 0.9.42
                                              • Index
                                                • diff --git a/inst/web/mkinplot.html b/inst/web/mkinplot.html index c8787242..c4542072 100644 --- a/inst/web/mkinplot.html +++ b/inst/web/mkinplot.html @@ -2,7 +2,7 @@ -mkinplot. mkin 0.9.41.9000 +mkinplot. mkin 0.9.42
                                                - mkin 0.9.41.9000 + mkin 0.9.42
                                                • Index
                                                  • diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index 393c1e26..34c715f8 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -2,7 +2,7 @@ -mkinpredict. mkin 0.9.41.9000 +mkinpredict. mkin 0.9.42
                                                  - mkin 0.9.41.9000 + mkin 0.9.42
                                                  • Index
                                                    • @@ -304,7 +304,7 @@ 201 20 4.978707 27.46227
                                                  user system elapsed - 0.012 0.016 0.004 + 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 - 0.016 0.004 0.003 + 0.000 0.020 0.003
                                                  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 - 0.048 0.004 0.053 + 0.052 0.000 0.052
                                                  diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index ec82518b..5a2388dc 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9.41.9000 +mkinresplot. mkin 0.9.42
                                                  - mkin 0.9.41.9000 + mkin 0.9.42
                                                  • Index
                                                    • diff --git a/inst/web/mkinsub.html b/inst/web/mkinsub.html index 73b19907..2b92fbbc 100644 --- a/inst/web/mkinsub.html +++ b/inst/web/mkinsub.html @@ -2,7 +2,7 @@ -mkinsub. mkin 0.9.41.9000 +mkinsub. mkin 0.9.42
                                                    - mkin 0.9.41.9000 + mkin 0.9.42
                                                    • Index
                                                      • diff --git a/inst/web/mmkin.html b/inst/web/mmkin.html index cec39fc8..754be268 100644 --- a/inst/web/mmkin.html +++ b/inst/web/mmkin.html @@ -2,7 +2,7 @@ -mmkin. mkin 0.9.41.9000 +mmkin. mkin 0.9.42
                                                      - mkin 0.9.41.9000 + mkin 0.9.42
                                                      • Index
                                                        • diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html index 8acf1e19..1da0c8e8 100644 --- a/inst/web/plot.mkinfit.html +++ b/inst/web/plot.mkinfit.html @@ -2,7 +2,7 @@ -plot.mkinfit. mkin 0.9.41.9000 +plot.mkinfit. mkin 0.9.42
                                                        - mkin 0.9.41.9000 + mkin 0.9.42
                                                        • Index
                                                          • diff --git a/inst/web/plot.mmkin.html b/inst/web/plot.mmkin.html index 11a1ba54..587bf894 100644 --- a/inst/web/plot.mmkin.html +++ b/inst/web/plot.mmkin.html @@ -2,7 +2,7 @@ -plot.mmkin. mkin 0.9.41.9000 +plot.mmkin. mkin 0.9.42
                                                          - mkin 0.9.41.9000 + mkin 0.9.42
                                                          • Index
                                                            • diff --git a/inst/web/print.mkinds.html b/inst/web/print.mkinds.html index fdaaa64a..285684fd 100644 --- a/inst/web/print.mkinds.html +++ b/inst/web/print.mkinds.html @@ -2,7 +2,7 @@ -print.mkinds. mkin 0.9.41.9000 +print.mkinds. mkin 0.9.42 @@ -32,7 +32,7 @@
                                                            - mkin 0.9.41.9000 + mkin 0.9.42
                                                            • Index
                                                              • diff --git a/inst/web/print.mkinmod.html b/inst/web/print.mkinmod.html index 457ac78f..d773050d 100644 --- a/inst/web/print.mkinmod.html +++ b/inst/web/print.mkinmod.html @@ -2,7 +2,7 @@ -print.mkinmod. mkin 0.9.41.9000 +print.mkinmod. mkin 0.9.42 @@ -32,7 +32,7 @@
                                                              - mkin 0.9.41.9000 + mkin 0.9.42
                                                              • Index
                                                                • diff --git a/inst/web/schaefer07_complex_case.html b/inst/web/schaefer07_complex_case.html index e23bc962..c6b9e980 100644 --- a/inst/web/schaefer07_complex_case.html +++ b/inst/web/schaefer07_complex_case.html @@ -2,7 +2,7 @@ -schaefer07_complex_case. mkin 0.9.41.9000 +schaefer07_complex_case. mkin 0.9.42 @@ -32,7 +32,7 @@
                                                                - mkin 0.9.41.9000 + mkin 0.9.42
                                                                • Index
                                                                  • diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index 9771ff5b..69edb2fe 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -2,7 +2,7 @@ -summary.mkinfit. mkin 0.9.41.9000 +summary.mkinfit. mkin 0.9.42
                                                                  - mkin 0.9.41.9000 + mkin 0.9.42
                                                                  • Index
                                                                    • @@ -157,17 +157,17 @@

                                                                    Examples

                                                                      summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
 
                                                                    
-
                                                                    mkin version:    0.9.41.9000 
-R version:       3.2.2 
-Date of fit:     Wed Dec  9 10:17:07 2015 
-Date of summary: Wed Dec  9 10:17:07 2015 
+
                                                                    mkin version:    0.9.42 
+R version:       3.2.4 
+Date of fit:     Wed Mar 23 16:59:53 2016 
+Date of summary: Wed Mar 23 16:59:53 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 35 model solutions performed in 0.15 s
+Fitted with method Port using 35 model solutions performed in 0.102 s
 
 Weighting: none
 
diff --git a/inst/web/synthetic_data_for_UBA.html b/inst/web/synthetic_data_for_UBA.html
index 2ae4c868..9fb9d23e 100644
--- a/inst/web/synthetic_data_for_UBA.html
+++ b/inst/web/synthetic_data_for_UBA.html
@@ -2,7 +2,7 @@
 
   
     
-synthetic_data_for_UBA_2014. mkin 0.9.41.9000
+synthetic_data_for_UBA_2014. mkin 0.9.42
 
 
 
@@ -32,7 +32,7 @@
     
                                                                    
   
                                                                    
     
                                                                    
-      mkin 0.9.41.9000
+      mkin 0.9.42
       
                                                                    
         
                                                                      
           
                                                                    •  Index
                                                                      • 
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index 50ce71a7..81d3927f 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -2,7 +2,7 @@
 
   
     
-transform_odeparms. mkin 0.9.41.9000
+transform_odeparms. mkin 0.9.42
 
 
   
                                                                      
     
                                                                      
-      mkin 0.9.41.9000
+      mkin 0.9.42
       
                                                                      
         
                                                                        
           
                                                                      •  Index
                                                                        • 
@@ -133,10 +133,10 @@ backtransform_odeparms(transparms, mkinmod,  transform_rates = TRUE, t
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
 
                                                                      
-
                                                                      mkin version:    0.9.41.9000 
-R version:       3.2.2 
-Date of fit:     Wed Dec  9 10:17:08 2015 
-Date of summary: Wed Dec  9 10:17:08 2015 
+
                                                                      mkin version:    0.9.42 
+R version:       3.2.4 
+Date of fit:     Wed Mar 23 16:59:54 2016 
+Date of summary: Wed Mar 23 16:59:54 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 0.626 s
+Fitted with method Port using 153 model solutions performed in 0.667 s
 
 Weighting: none
 
diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html
index 076ab4c5..1f3c6677 100644
--- a/inst/web/vignettes/FOCUS_D.html
+++ b/inst/web/vignettes/FOCUS_D.html
@@ -10,20 +10,20 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Example Dataset D
 
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+
 
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-
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