From a7600ca6d4e5dfa62a16102f5a965f5e9891cf28 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Tue, 28 Jun 2016 10:32:31 +0200 Subject: Bump version for new release, rebuild static docs The test test_FOMC_ill-defined leads to errors on several architectures/distributions, as apparent from CRAN checks, so we need a new release. Static documentation rebuilt by staticdocs::build_site() --- DESCRIPTION | 2 +- build.log | 7 +--- 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 | 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 | 8 ++--- inst/web/vignettes/FOCUS_L.html | 56 +++++++++++++++---------------- inst/web/vignettes/FOCUS_Z.pdf | Bin 238788 -> 238789 bytes inst/web/vignettes/compiled_models.html | 38 ++++++++++----------- vignettes/FOCUS_D.html | 8 ++--- vignettes/FOCUS_L.html | 56 +++++++++++++++---------------- vignettes/FOCUS_Z.pdf | Bin 238788 -> 238789 bytes vignettes/compiled_models.html | 38 ++++++++++----------- 48 files changed, 212 insertions(+), 217 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index eb3c0b27..ef30256e 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 0.9.43.9000 +Version: 0.9.44 Date: 2016-06-28 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), diff --git a/build.log b/build.log index 2ba22f71..c3b0aa75 100644 --- a/build.log +++ b/build.log @@ -2,9 +2,4 @@ * preparing ‘mkin’: * checking DESCRIPTION meta-information ... OK * installing the package to build vignettes -* creating vignettes ... OK -* checking for LF line-endings in source and make files -* checking for empty or unneeded directories -* looking to see if a ‘data/datalist’ file should be added -* building ‘mkin_0.9.43.tar.gz’ - +* creating vignettes ... \ No newline at end of file diff --git a/inst/web/DFOP.solution.html b/inst/web/DFOP.solution.html index f9fc1ea8..f6d32d70 100644 --- a/inst/web/DFOP.solution.html +++ b/inst/web/DFOP.solution.html @@ -2,7 +2,7 @@ -DFOP.solution. mkin 0.9.43.9000 +DFOP.solution. mkin 0.9.44 @@ -32,7 +32,7 @@
- mkin 0.9.43.9000 + mkin 0.9.44
  • Index
    • diff --git a/inst/web/Extract.mmkin.html b/inst/web/Extract.mmkin.html index 71d5957b..134bb4cb 100644 --- a/inst/web/Extract.mmkin.html +++ b/inst/web/Extract.mmkin.html @@ -2,7 +2,7 @@ -[.mmkin. mkin 0.9.43.9000 +[.mmkin. mkin 0.9.44
    - mkin 0.9.43.9000 + mkin 0.9.44
    • Index
      • @@ -181,7 +181,7 @@ $calls $time user system elapsed - 0.696 0.000 0.698 + 0.712 0.004 0.716 $mkinmod <mkinmod> model generated with @@ -367,7 +367,7 @@ function (P) } return(mC) } -<environment: 0x3b92678> +<environment: 0x48ad868> $cost_notrans function (P) @@ -389,7 +389,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x3b92678> +<environment: 0x48ad868> $hessian_notrans parent_0 alpha beta @@ -455,7 +455,7 @@ $bparms.state 99.66619 $date -[1] "Tue Jun 28 08:14:11 2016" +[1] "Tue Jun 28 10:24:49 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -540,7 +540,7 @@ $calls $time user system elapsed - 0.256 0.000 0.253 + 0.204 0.000 0.205 $mkinmod <mkinmod> model generated with @@ -727,7 +727,7 @@ function (P) } return(mC) } -<environment: 0x41e0de0> +<environment: 0x561e810> $cost_notrans function (P) @@ -749,7 +749,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x41e0de0> +<environment: 0x561e810> $hessian_notrans parent_0 k_parent_sink @@ -812,7 +812,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 08:14:11 2016" +[1] "Tue Jun 28 10:24:48 2016" attr(,"class") [1] "mkinfit" "modFit" @@ -890,7 +890,7 @@ $calls $time user system elapsed - 0.256 0.000 0.253 + 0.204 0.000 0.205 $mkinmod <mkinmod> model generated with @@ -1077,7 +1077,7 @@ function (P) } return(mC) } -<environment: 0x41e0de0> +<environment: 0x561e810> $cost_notrans function (P) @@ -1099,7 +1099,7 @@ function (P) scaleVar = scaleVar) return(mC) } -<environment: 0x41e0de0> +<environment: 0x561e810> $hessian_notrans parent_0 k_parent_sink @@ -1162,7 +1162,7 @@ $bparms.state 99.17407 $date -[1] "Tue Jun 28 08:14:11 2016" +[1] "Tue Jun 28 10:24:48 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 f3a19618..2a4de917 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 0.9.43.9000 +FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.44 @@ -32,7 +32,7 @@
      - mkin 0.9.43.9000 + mkin 0.9.44
      • 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 84941896..f5860202 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 0.9.43.9000 +FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.44 @@ -32,7 +32,7 @@
        - mkin 0.9.43.9000 + mkin 0.9.44
        • 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 b79dd2d3..4894a54a 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 0.9.43.9000 +FOCUS_2006_HS_ref_A_to_F. mkin 0.9.44 @@ -32,7 +32,7 @@
          - mkin 0.9.43.9000 + mkin 0.9.44
          • 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 fc7191b5..45012d12 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 0.9.43.9000 +FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.44 @@ -32,7 +32,7 @@
            - mkin 0.9.43.9000 + mkin 0.9.44
            • Index
              • diff --git a/inst/web/FOCUS_2006_datasets.html b/inst/web/FOCUS_2006_datasets.html index 4c87b181..abb38738 100644 --- a/inst/web/FOCUS_2006_datasets.html +++ b/inst/web/FOCUS_2006_datasets.html @@ -2,7 +2,7 @@ -FOCUS_2006_datasets. mkin 0.9.43.9000 +FOCUS_2006_datasets. mkin 0.9.44 @@ -32,7 +32,7 @@
              - mkin 0.9.43.9000 + mkin 0.9.44
              • Index
                • diff --git a/inst/web/FOMC.solution.html b/inst/web/FOMC.solution.html index ae9f60f0..a8a80911 100644 --- a/inst/web/FOMC.solution.html +++ b/inst/web/FOMC.solution.html @@ -2,7 +2,7 @@ -FOMC.solution. mkin 0.9.43.9000 +FOMC.solution. mkin 0.9.44 @@ -32,7 +32,7 @@
                - mkin 0.9.43.9000 + mkin 0.9.44
                • Index
                  • diff --git a/inst/web/HS.solution.html b/inst/web/HS.solution.html index 593b2fb4..0ed5779f 100644 --- a/inst/web/HS.solution.html +++ b/inst/web/HS.solution.html @@ -2,7 +2,7 @@ -HS.solution. mkin 0.9.43.9000 +HS.solution. mkin 0.9.44 @@ -32,7 +32,7 @@
                  - mkin 0.9.43.9000 + mkin 0.9.44
                  • Index
                    • diff --git a/inst/web/IORE.solution.html b/inst/web/IORE.solution.html index 825ae816..45f01ac1 100644 --- a/inst/web/IORE.solution.html +++ b/inst/web/IORE.solution.html @@ -2,7 +2,7 @@ -IORE.solution. mkin 0.9.43.9000 +IORE.solution. mkin 0.9.44 @@ -32,7 +32,7 @@
                    - mkin 0.9.43.9000 + mkin 0.9.44
                    • Index
                      • diff --git a/inst/web/SFO.solution.html b/inst/web/SFO.solution.html index ca866ddc..c740a6e5 100644 --- a/inst/web/SFO.solution.html +++ b/inst/web/SFO.solution.html @@ -2,7 +2,7 @@ -SFO.solution. mkin 0.9.43.9000 +SFO.solution. mkin 0.9.44 @@ -32,7 +32,7 @@
                      - mkin 0.9.43.9000 + mkin 0.9.44
                      • Index
                        • diff --git a/inst/web/SFORB.solution.html b/inst/web/SFORB.solution.html index 74e7370c..10de4783 100644 --- a/inst/web/SFORB.solution.html +++ b/inst/web/SFORB.solution.html @@ -2,7 +2,7 @@ -SFORB.solution. mkin 0.9.43.9000 +SFORB.solution. mkin 0.9.44 @@ -32,7 +32,7 @@
                        - mkin 0.9.43.9000 + mkin 0.9.44
                        • Index
                          • diff --git a/inst/web/add_err.html b/inst/web/add_err.html index da3a85b7..1ab38bb8 100644 --- a/inst/web/add_err.html +++ b/inst/web/add_err.html @@ -2,7 +2,7 @@ -add_err. mkin 0.9.43.9000 +add_err. mkin 0.9.44
                          - mkin 0.9.43.9000 + mkin 0.9.44
                          • Index
                            • diff --git a/inst/web/endpoints.html b/inst/web/endpoints.html index b57874e3..4835f156 100644 --- a/inst/web/endpoints.html +++ b/inst/web/endpoints.html @@ -2,7 +2,7 @@ -endpoints. mkin 0.9.43.9000 +endpoints. mkin 0.9.44
                            - mkin 0.9.43.9000 + mkin 0.9.44
                            • Index
                              • diff --git a/inst/web/geometric_mean.html b/inst/web/geometric_mean.html index a0c7610e..ec6c3704 100644 --- a/inst/web/geometric_mean.html +++ b/inst/web/geometric_mean.html @@ -2,7 +2,7 @@ -geometric_mean. mkin 0.9.43.9000 +geometric_mean. mkin 0.9.44 @@ -32,7 +32,7 @@
                              - mkin 0.9.43.9000 + mkin 0.9.44
                              • Index
                                • diff --git a/inst/web/ilr.html b/inst/web/ilr.html index 6c446569..baa5ed74 100644 --- a/inst/web/ilr.html +++ b/inst/web/ilr.html @@ -2,7 +2,7 @@ -ilr. mkin 0.9.43.9000 +ilr. mkin 0.9.44
                                - mkin 0.9.43.9000 + mkin 0.9.44
                                • Index
                                  • diff --git a/inst/web/index.html b/inst/web/index.html index 896373f2..22afd22e 100644 --- a/inst/web/index.html +++ b/inst/web/index.html @@ -2,7 +2,7 @@ -Index. mkin 0.9.43.9000 +Index. mkin 0.9.44 @@ -32,7 +32,7 @@
                                  - mkin 0.9.43.9000 + mkin 0.9.44
                                  • Index
                                    • diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 335af648..09609b0c 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -2,7 +2,7 @@ -mccall81_245T. mkin 0.9.43.9000 +mccall81_245T. mkin 0.9.44 @@ -32,7 +32,7 @@
                                    - mkin 0.9.43.9000 + mkin 0.9.44
                                    • Index
                                      • @@ -112,10 +112,10 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
                                    -
                                    mkin version: 0.9.43.9000 +
                                    mkin version: 0.9.44 R version: 3.3.1 -Date of fit: Tue Jun 28 08:14:29 2016 -Date of summary: Tue Jun 28 08:14:29 2016 +Date of fit: Tue Jun 28 10:25:07 2016 +Date of summary: Tue Jun 28 10:25:08 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 3.812 s +Fitted with method Port using 246 model solutions performed in 3.86 s Weighting: none diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index 8ce17568..7109f1c9 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 0.9.43.9000 +mkin_long_to_wide. mkin 0.9.44
                                    - mkin 0.9.43.9000 + mkin 0.9.44
                                    • Index
                                      • diff --git a/inst/web/mkin_wide_to_long.html b/inst/web/mkin_wide_to_long.html index fbc468fe..d783d5a2 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 0.9.43.9000 +mkin_wide_to_long. mkin 0.9.44
                                      - mkin 0.9.43.9000 + mkin 0.9.44
                                      • Index
                                        • diff --git a/inst/web/mkinds.html b/inst/web/mkinds.html index 5db3b179..6021dd89 100644 --- a/inst/web/mkinds.html +++ b/inst/web/mkinds.html @@ -2,7 +2,7 @@ -mkinds. mkin 0.9.43.9000 +mkinds. mkin 0.9.44 @@ -32,7 +32,7 @@
                                        - mkin 0.9.43.9000 + mkin 0.9.44
                                        • Index
                                          • diff --git a/inst/web/mkinerrmin.html b/inst/web/mkinerrmin.html index b82caae8..5cab6f43 100644 --- a/inst/web/mkinerrmin.html +++ b/inst/web/mkinerrmin.html @@ -2,7 +2,7 @@ -mkinerrmin. mkin 0.9.43.9000 +mkinerrmin. mkin 0.9.44 @@ -32,7 +32,7 @@
                                          - mkin 0.9.43.9000 + mkin 0.9.44
                                          • Index
                                            • diff --git a/inst/web/mkinfit.html b/inst/web/mkinfit.html index 2d13317a..89b22754 100644 --- a/inst/web/mkinfit.html +++ b/inst/web/mkinfit.html @@ -2,7 +2,7 @@ -mkinfit. mkin 0.9.43.9000 +mkinfit. mkin 0.9.44
                                            - mkin 0.9.43.9000 + mkin 0.9.44
                                            • Index
                                              • @@ -323,17 +323,17 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
                                            -
                                            mkin version: 0.9.43.9000 +
                                            mkin version: 0.9.44 R version: 3.3.1 -Date of fit: Tue Jun 28 08:14:35 2016 -Date of summary: Tue Jun 28 08:14:35 2016 +Date of fit: Tue Jun 28 10:25:14 2016 +Date of summary: Tue Jun 28 10:25:14 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 0.438 s +Fitted with method Port using 64 model solutions performed in 0.44 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 2.244 2.238 + 2.852 2.240 2.272
                                            coef(fit)
                                            diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index 714975c1..04b4a453 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9.43.9000 +mkinmod. mkin 0.9.44
                                            - mkin 0.9.43.9000 + mkin 0.9.44
                                            • Index
                                              • diff --git a/inst/web/mkinparplot.html b/inst/web/mkinparplot.html index e5a91e3a..45eb9850 100644 --- a/inst/web/mkinparplot.html +++ b/inst/web/mkinparplot.html @@ -2,7 +2,7 @@ -mkinparplot. mkin 0.9.43.9000 +mkinparplot. mkin 0.9.44
                                              - mkin 0.9.43.9000 + mkin 0.9.44
                                              • Index
                                                • diff --git a/inst/web/mkinplot.html b/inst/web/mkinplot.html index 3a45bea8..b84b62f9 100644 --- a/inst/web/mkinplot.html +++ b/inst/web/mkinplot.html @@ -2,7 +2,7 @@ -mkinplot. mkin 0.9.43.9000 +mkinplot. mkin 0.9.44
                                                - mkin 0.9.43.9000 + mkin 0.9.44
                                                • Index
                                                  • diff --git a/inst/web/mkinpredict.html b/inst/web/mkinpredict.html index 718aad5d..728c4e10 100644 --- a/inst/web/mkinpredict.html +++ b/inst/web/mkinpredict.html @@ -2,7 +2,7 @@ -mkinpredict. mkin 0.9.43.9000 +mkinpredict. mkin 0.9.44
                                                  - mkin 0.9.43.9000 + mkin 0.9.44
                                                  • Index
                                                    • @@ -304,7 +304,7 @@ 201 20 4.978707 27.46227
                                                  user system elapsed - 0.028 0.044 0.011 + 0.032 0.040 0.011
                                                  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 0.004 0.004 + 0.000 0.020 0.005
                                                  system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -326,7 +326,7 @@ 201 20 4.978707 27.46227
                                                  user system elapsed - 0.136 0.004 0.138 + 0.140 0.000 0.139
                                                  diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index 6619c0b9..49769d62 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9.43.9000 +mkinresplot. mkin 0.9.44
                                                  - mkin 0.9.43.9000 + mkin 0.9.44
                                                  • Index
                                                    • diff --git a/inst/web/mkinsub.html b/inst/web/mkinsub.html index 1c7ca30a..6fbd12f8 100644 --- a/inst/web/mkinsub.html +++ b/inst/web/mkinsub.html @@ -2,7 +2,7 @@ -mkinsub. mkin 0.9.43.9000 +mkinsub. mkin 0.9.44
                                                    - mkin 0.9.43.9000 + mkin 0.9.44
                                                    • Index
                                                      • diff --git a/inst/web/mmkin.html b/inst/web/mmkin.html index f600ffd3..a8a5499b 100644 --- a/inst/web/mmkin.html +++ b/inst/web/mmkin.html @@ -2,7 +2,7 @@ -mmkin. mkin 0.9.43.9000 +mmkin. mkin 0.9.44
                                                      - mkin 0.9.43.9000 + mkin 0.9.44
                                                      • Index
                                                        • diff --git a/inst/web/plot.mkinfit.html b/inst/web/plot.mkinfit.html index 6a37657f..938963af 100644 --- a/inst/web/plot.mkinfit.html +++ b/inst/web/plot.mkinfit.html @@ -2,7 +2,7 @@ -plot.mkinfit. mkin 0.9.43.9000 +plot.mkinfit. mkin 0.9.44
                                                        - mkin 0.9.43.9000 + mkin 0.9.44
                                                        • Index
                                                          • diff --git a/inst/web/plot.mmkin.html b/inst/web/plot.mmkin.html index c12f92f2..070892b0 100644 --- a/inst/web/plot.mmkin.html +++ b/inst/web/plot.mmkin.html @@ -2,7 +2,7 @@ -plot.mmkin. mkin 0.9.43.9000 +plot.mmkin. mkin 0.9.44
                                                          - mkin 0.9.43.9000 + mkin 0.9.44
                                                          • Index
                                                            • diff --git a/inst/web/print.mkinds.html b/inst/web/print.mkinds.html index 523e1e67..f582702b 100644 --- a/inst/web/print.mkinds.html +++ b/inst/web/print.mkinds.html @@ -2,7 +2,7 @@ -print.mkinds. mkin 0.9.43.9000 +print.mkinds. mkin 0.9.44 @@ -32,7 +32,7 @@
                                                            - mkin 0.9.43.9000 + mkin 0.9.44
                                                            • Index
                                                              • diff --git a/inst/web/print.mkinmod.html b/inst/web/print.mkinmod.html index ca4e5d36..7e0d8140 100644 --- a/inst/web/print.mkinmod.html +++ b/inst/web/print.mkinmod.html @@ -2,7 +2,7 @@ -print.mkinmod. mkin 0.9.43.9000 +print.mkinmod. mkin 0.9.44 @@ -32,7 +32,7 @@
                                                              - mkin 0.9.43.9000 + mkin 0.9.44
                                                              • Index
                                                                • diff --git a/inst/web/schaefer07_complex_case.html b/inst/web/schaefer07_complex_case.html index 2e5d91a2..387dac46 100644 --- a/inst/web/schaefer07_complex_case.html +++ b/inst/web/schaefer07_complex_case.html @@ -2,7 +2,7 @@ -schaefer07_complex_case. mkin 0.9.43.9000 +schaefer07_complex_case. mkin 0.9.44 @@ -32,7 +32,7 @@
                                                                - mkin 0.9.43.9000 + mkin 0.9.44
                                                                • Index
                                                                  • diff --git a/inst/web/summary.mkinfit.html b/inst/web/summary.mkinfit.html index fade0f56..dfa939ae 100644 --- a/inst/web/summary.mkinfit.html +++ b/inst/web/summary.mkinfit.html @@ -2,7 +2,7 @@ -summary.mkinfit. mkin 0.9.43.9000 +summary.mkinfit. mkin 0.9.44
                                                                  - mkin 0.9.43.9000 + mkin 0.9.44
                                                                  • Index
                                                                    • @@ -157,17 +157,17 @@

                                                                    Examples

                                                                      summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
 
                                                                    
-
                                                                    mkin version:    0.9.43.9000 
+
                                                                    mkin version:    0.9.44 
 R version:       3.3.1 
-Date of fit:     Tue Jun 28 08:14:56 2016 
-Date of summary: Tue Jun 28 08:14:56 2016 
+Date of fit:     Tue Jun 28 10:25:34 2016 
+Date of summary: Tue Jun 28 10:25:34 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 35 model solutions performed in 0.244 s
+Fitted with method Port using 35 model solutions performed in 0.286 s
 
 Weighting: none
 
diff --git a/inst/web/synthetic_data_for_UBA.html b/inst/web/synthetic_data_for_UBA.html
index 2daf00ff..0d0326a5 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 0.9.43.9000
+synthetic_data_for_UBA_2014. mkin 0.9.44
 
 
 
@@ -32,7 +32,7 @@
     
                                                                    
   
                                                                    
     
                                                                    
-      mkin 0.9.43.9000
+      mkin 0.9.44
       
                                                                    
         
                                                                      
           
                                                                    •  Index
                                                                      • 
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index 50dd8ad4..b1207f6a 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -2,7 +2,7 @@
 
   
     
-transform_odeparms. mkin 0.9.43.9000
+transform_odeparms. mkin 0.9.44
 
 
   
                                                                      
     
                                                                      
-      mkin 0.9.43.9000
+      mkin 0.9.44
       
                                                                      
         
                                                                        
           
                                                                      •  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:    0.9.43.9000 
+
                                                                      mkin version:    0.9.44 
 R version:       3.3.1 
-Date of fit:     Tue Jun 28 08:14:58 2016 
-Date of summary: Tue Jun 28 08:14:58 2016 
+Date of fit:     Tue Jun 28 10:25:37 2016 
+Date of summary: Tue Jun 28 10:25:37 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 1.67 s
+Fitted with method Port using 153 model solutions performed in 1.788 s
 
 Weighting: none
 
diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html
index c7e2047f..d60d1c7f 100644
--- a/inst/web/vignettes/FOCUS_D.html
+++ b/inst/web/vignettes/FOCUS_D.html
@@ -190,10 +190,10 @@ print(FOCUS_2006_D)

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

                                                                    summary(fit)
                                                                    -
                                                                    ## mkin version:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:31 2016 
-## Date of summary: Tue Jun 28 08:19:31 2016 
+## Date of fit:     Tue Jun 28 10:30:09 2016 
+## Date of summary: Tue Jun 28 10:30:09 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 1.706 s
+## Fitted with method Port using 153 model solutions performed in 1.707 s
 ## 
 ## Weighting: none
 ## 
diff --git a/inst/web/vignettes/FOCUS_L.html b/inst/web/vignettes/FOCUS_L.html
index 05b9bdbd..4c509eb2 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:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:32 2016 
-## Date of summary: Tue Jun 28 08:19:32 2016 
+## Date of fit:     Tue Jun 28 10:30:10 2016 
+## Date of summary: Tue Jun 28 10:30:10 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.245 s
+## Fitted with method Port using 37 model solutions performed in 0.249 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:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:34 2016 
-## Date of summary: Tue Jun 28 08:19:34 2016 
+## Date of fit:     Tue Jun 28 10:30:12 2016 
+## Date of summary: Tue Jun 28 10:30:12 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 1.216 s
+## Fitted with method Port using 188 model solutions performed in 1.227 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:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:36 2016 
-## Date of summary: Tue Jun 28 08:19:36 2016 
+## Date of fit:     Tue Jun 28 10:30:14 2016 
+## Date of summary: Tue Jun 28 10:30:14 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 0.537 s
+## Fitted with method Port using 81 model solutions performed in 0.543 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:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:39 2016 
-## Date of summary: Tue Jun 28 08:19:39 2016 
+## Date of fit:     Tue Jun 28 10:30:17 2016 
+## Date of summary: Tue Jun 28 10:30:17 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 2.267 s
+## Fitted with method Port using 336 model solutions performed in 2.274 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:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:41 2016 
-## Date of summary: Tue Jun 28 08:19:42 2016 
+## Date of fit:     Tue Jun 28 10:30:19 2016 
+## Date of summary: Tue Jun 28 10:30:20 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 0.924 s
+## Fitted with method Port using 137 model solutions performed in 0.898 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:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:42 2016 
-## Date of summary: Tue Jun 28 08:19:43 2016 
+## Date of fit:     Tue Jun 28 10:30:20 2016 
+## Date of summary: Tue Jun 28 10:30:21 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.307 s
+## Fitted with method Port using 46 model solutions performed in 0.302 s
 ## 
 ## Weighting: none
 ## 
@@ -742,17 +742,17 @@ plot(mm.L4)
                                                                    
 ##        DT50 DT90
 ## parent  106  352
                                                                    
 
                                                                    summary(mm.L4[["FOMC", 1]], data = FALSE)
                                                                    
-
                                                                    ## mkin version:    0.9.43.9000 
+
                                                                    ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:43 2016 
-## Date of summary: Tue Jun 28 08:19:43 2016 
+## Date of fit:     Tue Jun 28 10:30:21 2016 
+## Date of summary: Tue Jun 28 10:30:21 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 0.414 s
+## Fitted with method Port using 66 model solutions performed in 0.425 s
 ## 
 ## Weighting: none
 ## 
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index 1f9560b0..af86c965 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 cec76ef9..12289676 100644
--- a/inst/web/vignettes/compiled_models.html
+++ b/inst/web/vignettes/compiled_models.html
@@ -250,21 +250,21 @@ mb.1 <- microbenchmark(
 print(mb.1)
                                                                    
 
                                                                    ## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  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
                                                                    
+##  deSolve, not compiled 25.120822 25.185794 25.345704 25.250766 25.458146
+##       Eigenvalue based  2.246793  2.255533  2.258865  2.264274  2.264901
+##      deSolve, compiled  1.861661  1.893380  1.930436  1.925098  1.964823
+##        max neval cld
+##  25.665525     3   b
+##   2.265527     3  a 
+##   2.004547     3  a
                                                                    
 
                                                                    autoplot(mb.1)
                                                                    
-
                                                                    
-
                                                                    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:
                                                                    
+
                                                                    
+
                                                                    We see that using the compiled model is by a factor of 13.1 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 14.010730
-## Eigenvalue based       1.204226
+## deSolve, not compiled 13.116611
+## Eigenvalue based       1.176186
 ## 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 54.386189 54.39423 54.477986 54.402271 54.523884
-##      deSolve, compiled  3.424205  3.53522  3.574587  3.646236  3.649778
+##                   expr       min        lq      mean    median        uq
+##  deSolve, not compiled 54.536624 54.617928 54.690830 54.699231 54.767933
+##      deSolve, compiled  3.690661  3.693247  3.720722  3.695833  3.735753
 ##        max neval cld
-##  54.645498     3   b
-##   3.653319     3  a
                                                                  +## 54.836635 3 b +## 3.775673 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 0.9.43.9000 on

                                                                  +

                                                                  +

                                                                  Here we get a performance benefit of a factor of 14.8 using the version of the differential equation model compiled from C code!

                                                                  +

                                                                  This vignette was built with mkin 0.9.44 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/FOCUS_D.html b/vignettes/FOCUS_D.html index c7e2047f..d60d1c7f 100644 --- a/vignettes/FOCUS_D.html +++ b/vignettes/FOCUS_D.html @@ -190,10 +190,10 @@ print(FOCUS_2006_D)

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

                                                                  summary(fit)
                                                                  -
                                                                  ## mkin version:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:31 2016 
-## Date of summary: Tue Jun 28 08:19:31 2016 
+## Date of fit:     Tue Jun 28 10:30:09 2016 
+## Date of summary: Tue Jun 28 10:30:09 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 1.706 s
+## Fitted with method Port using 153 model solutions performed in 1.707 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html
index 05b9bdbd..4c509eb2 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:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:32 2016 
-## Date of summary: Tue Jun 28 08:19:32 2016 
+## Date of fit:     Tue Jun 28 10:30:10 2016 
+## Date of summary: Tue Jun 28 10:30:10 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.245 s
+## Fitted with method Port using 37 model solutions performed in 0.249 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:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:34 2016 
-## Date of summary: Tue Jun 28 08:19:34 2016 
+## Date of fit:     Tue Jun 28 10:30:12 2016 
+## Date of summary: Tue Jun 28 10:30:12 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 1.216 s
+## Fitted with method Port using 188 model solutions performed in 1.227 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:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:36 2016 
-## Date of summary: Tue Jun 28 08:19:36 2016 
+## Date of fit:     Tue Jun 28 10:30:14 2016 
+## Date of summary: Tue Jun 28 10:30:14 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 0.537 s
+## Fitted with method Port using 81 model solutions performed in 0.543 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:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:39 2016 
-## Date of summary: Tue Jun 28 08:19:39 2016 
+## Date of fit:     Tue Jun 28 10:30:17 2016 
+## Date of summary: Tue Jun 28 10:30:17 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 2.267 s
+## Fitted with method Port using 336 model solutions performed in 2.274 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:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:41 2016 
-## Date of summary: Tue Jun 28 08:19:42 2016 
+## Date of fit:     Tue Jun 28 10:30:19 2016 
+## Date of summary: Tue Jun 28 10:30:20 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 0.924 s
+## Fitted with method Port using 137 model solutions performed in 0.898 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:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:42 2016 
-## Date of summary: Tue Jun 28 08:19:43 2016 
+## Date of fit:     Tue Jun 28 10:30:20 2016 
+## Date of summary: Tue Jun 28 10:30:21 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.307 s
+## Fitted with method Port using 46 model solutions performed in 0.302 s
 ## 
 ## Weighting: none
 ## 
@@ -742,17 +742,17 @@ plot(mm.L4)
                                                                  
 ##        DT50 DT90
 ## parent  106  352
                                                                  
 
                                                                  summary(mm.L4[["FOMC", 1]], data = FALSE)
                                                                  
-
                                                                  ## mkin version:    0.9.43.9000 
+
                                                                  ## mkin version:    0.9.44 
 ## R version:       3.3.1 
-## Date of fit:     Tue Jun 28 08:19:43 2016 
-## Date of summary: Tue Jun 28 08:19:43 2016 
+## Date of fit:     Tue Jun 28 10:30:21 2016 
+## Date of summary: Tue Jun 28 10:30:21 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 0.414 s
+## Fitted with method Port using 66 model solutions performed in 0.425 s
 ## 
 ## Weighting: none
 ## 
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 1f9560b0..af86c965 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 cec76ef9..12289676 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -250,21 +250,21 @@ mb.1 <- microbenchmark(
 print(mb.1)
                                                                  
 
                                                                  ## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  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
                                                                  
+##  deSolve, not compiled 25.120822 25.185794 25.345704 25.250766 25.458146
+##       Eigenvalue based  2.246793  2.255533  2.258865  2.264274  2.264901
+##      deSolve, compiled  1.861661  1.893380  1.930436  1.925098  1.964823
+##        max neval cld
+##  25.665525     3   b
+##   2.265527     3  a 
+##   2.004547     3  a
                                                                  
 
                                                                  autoplot(mb.1)
                                                                  
-
                                                                  
-
                                                                  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:
                                                                  
+
                                                                  
+
                                                                  We see that using the compiled model is by a factor of 13.1 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 14.010730
-## Eigenvalue based       1.204226
+## deSolve, not compiled 13.116611
+## Eigenvalue based       1.176186
 ## 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 54.386189 54.39423 54.477986 54.402271 54.523884
-##      deSolve, compiled  3.424205  3.53522  3.574587  3.646236  3.649778
+##                   expr       min        lq      mean    median        uq
+##  deSolve, not compiled 54.536624 54.617928 54.690830 54.699231 54.767933
+##      deSolve, compiled  3.690661  3.693247  3.720722  3.695833  3.735753
 ##        max neval cld
-##  54.645498     3   b
-##   3.653319     3  a
                                                                  +## 54.836635 3 b +## 3.775673 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 0.9.43.9000 on

                                                                  +

                                                                  +

                                                                  Here we get a performance benefit of a factor of 14.8 using the version of the differential equation model compiled from C code!

                                                                  +

                                                                  This vignette was built with mkin 0.9.44 on

                                                                  ## R version 3.3.1 (2016-06-21)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 8 (jessie)
                                                                  -- cgit v1.2.1