From 20d7834a633d32b663c6bcc1a7f7b0300aa65d5b Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Sat, 29 Jul 2017 15:15:41 +0200 Subject: Bump version, update NEWS and rebuild pkdown docs --- DESCRIPTION | 4 +- NEWS.md | 14 +++++ build.log | 2 +- check.log | 2 +- docs/index.html | 2 +- docs/news/index.html | 19 ++++++ docs/reference/DFOP.solution-2.png | Bin 6375 -> 6748 bytes docs/reference/DFOP.solution.html | 2 +- docs/reference/Extract.mmkin.html | 14 ++--- docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html | 2 +- docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_HS_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_SFO_ref_A_to_F.html | 2 +- docs/reference/FOCUS_2006_datasets.html | 2 +- docs/reference/FOMC.solution-2.png | Bin 6406 -> 6774 bytes docs/reference/FOMC.solution.html | 2 +- docs/reference/HS.solution-2.png | Bin 6153 -> 6548 bytes docs/reference/HS.solution.html | 2 +- docs/reference/IORE.solution-2.png | Bin 6168 -> 6536 bytes docs/reference/SFO.solution-2.png | Bin 6424 -> 6779 bytes docs/reference/SFO.solution.html | 2 +- docs/reference/SFORB.solution-2.png | Bin 6788 -> 7164 bytes docs/reference/SFORB.solution.html | 2 +- docs/reference/add_err-4.png | Bin 26860 -> 28621 bytes docs/reference/add_err-6.png | Bin 15779 -> 16724 bytes docs/reference/add_err-8.png | Bin 14754 -> 15700 bytes docs/reference/index.html | 2 +- docs/reference/mccall81_245T.html | 20 +++--- docs/reference/mkinerrmin.html | 2 +- docs/reference/mkinfit.html | 72 +++++++++++----------- docs/reference/mkinmod.html | 4 +- docs/reference/mkinparplot-4.png | Bin 5360 -> 5812 bytes docs/reference/mkinpredict.html | 6 +- docs/reference/mkinresplot-4.png | Bin 5255 -> 5508 bytes docs/reference/mmkin-15.png | Bin 30012 -> 32054 bytes docs/reference/mmkin-17.png | Bin 27062 -> 29169 bytes docs/reference/mmkin-19.png | Bin 25359 -> 27180 bytes docs/reference/mmkin-21.png | Bin 18905 -> 20661 bytes docs/reference/mmkin-23.png | Bin 17039 -> 18163 bytes docs/reference/mmkin.html | 4 +- docs/reference/plot.mkinfit-10.png | Bin 18197 -> 19456 bytes docs/reference/plot.mkinfit-4.png | Bin 13748 -> 14285 bytes docs/reference/plot.mkinfit-6.png | Bin 16810 -> 17596 bytes docs/reference/plot.mkinfit-8.png | Bin 13728 -> 14529 bytes docs/reference/plot.mmkin-2.png | Bin 10552 -> 11258 bytes docs/reference/plot.mmkin-4.png | Bin 10559 -> 11349 bytes docs/reference/plot.mmkin-6.png | Bin 7945 -> 8386 bytes docs/reference/schaefer07_complex_case-4.png | Bin 18198 -> 18729 bytes docs/reference/summary.mkinfit.html | 12 ++-- docs/reference/synthetic_data_for_UBA.html | 10 +-- docs/reference/synthetic_data_for_UBA_2014-10.png | Bin 18905 -> 20661 bytes docs/reference/transform_odeparms.html | 40 ++++++------ 52 files changed, 141 insertions(+), 108 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 36a54b55..e18c3fea 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,8 +1,8 @@ Package: mkin Type: Package Title: Kinetic Evaluation of Chemical Degradation Data -Version: 0.9.45.2 -Date: 2017-07-21 +Version: 0.9.46 +Date: 2017-07-29 Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"), email = "jranke@uni-bremen.de"), person("Katrin", "Lindenberger", role = "ctb"), diff --git a/NEWS.md b/NEWS.md index ac36f39b..818a85be 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,17 @@ +# mkin 0.9.46 (2017-07-24) + +- Remove `test_FOMC_ill-defined.R` as it is too platform dependent + +# mkin 0.9.45.2 (2017-07-24) + +- Rename `twa` to `max_twa_parent` to avoid conflict with `twa` from my `pfm` package + +- Update URLs in documentation + +- Limit test code to one core to pass on windows + +- Switch from `microbenchmark` to `rbenchmark` as the former is not supported on all platforms + # mkin 0.9.45.1 (2016-12-20) ## New features diff --git a/build.log b/build.log index 4cdccab4..2d06c4dc 100644 --- a/build.log +++ b/build.log @@ -6,5 +6,5 @@ * 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_0.9.45.2.tar.gz’ +* building ‘mkin_0.9.46.tar.gz’ diff --git a/check.log b/check.log index 2876f64a..6db43c99 100644 --- a/check.log +++ b/check.log @@ -5,7 +5,7 @@ * using options ‘--no-tests --as-cran’ * checking for file ‘mkin/DESCRIPTION’ ... OK * checking extension type ... Package -* this is package ‘mkin’ version ‘0.9.45.2’ +* this is package ‘mkin’ version ‘0.9.45.3’ * package encoding: UTF-8 * checking CRAN incoming feasibility ... Note_to_CRAN_maintainers Maintainer: ‘Johannes Ranke ’ diff --git a/docs/index.html b/docs/index.html index 7ac6f226..9898d6f5 100644 --- a/docs/index.html +++ b/docs/index.html @@ -134,7 +134,7 @@

Credits and historical remarks

mkin would not be possible without the underlying software stack consisting of R and the packages deSolve and FME, to say the least.

-

It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

+

It could not have been written without me being introduced to regulatory fate modelling of pesticides by Adrian Gurney during my time at Harlan Laboratories Ltd (formerly RCC Ltd). mkin greatly profits from and largely follows the work done by the FOCUS Degradation Kinetics Workgroup, as detailed in their guidance document from 2006, slightly updated in 2011 and in 2014.

Also, it was inspired by the first version of KinGUI developed by BayerCropScience, which is based on the MatLab runtime environment.

The companion package kinfit (now deprecated) was started in 2008 and first published on CRAN on 01 May 2010.

The first mkin code was published on 11 May 2010 and the first CRAN version on 18 May 2010.

diff --git a/docs/news/index.html b/docs/news/index.html index 667c5c1f..b4f97681 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -105,6 +105,23 @@
+
+

+mkin 0.9.46 (2017-07-24)

+
    +
  • Remove test_FOMC_ill-defined.R as it is too platform dependent
    • +
+
+
+

+mkin 0.9.45.2 (2017-07-24)

+
    +

  • Rename twa to max_twa_parent to avoid conflict with twa from my pfm package

    • +

  • Update URLs in documentation

    • +

  • Limit test code to one core to pass on windows

    • +

  • Switch from microbenchmark to rbenchmark as the former is not supported on all platforms

    • +
+

mkin 0.9.45.1 (2016-12-20)

@@ -538,6 +555,8 @@

Contents

    +
  • 0.9.46
    • +
  • 0.9.45.2
  • 0.9.45.1
  • 0.9.45
  • 0.9.44
    • diff --git a/docs/reference/DFOP.solution-2.png b/docs/reference/DFOP.solution-2.png index 91efcebb..0902b9df 100644 Binary files a/docs/reference/DFOP.solution-2.png and b/docs/reference/DFOP.solution-2.png differ diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 3dbacdc1..30b9d057 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -146,7 +146,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index 135297cd..5d4eca29 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -398,7 +398,7 @@ #> { #> assign("calls", calls + 1, inherits = TRUE) #> if (trace_parms) -#> cat(P, "\n") +#> cat(P, "\\n") #> if (length(state.ini.optim) > 0) { #> odeini <- c(P[1:length(state.ini.optim)], state.ini.fixed) #> names(odeini) <- c(state.ini.optim.boxnames, state.ini.fixed.boxnames) @@ -420,7 +420,7 @@ #> if (mC$model < cost.old) { #> if (!quiet) #> cat("Model cost at call ", calls, ": ", mC$model, -#> "\n") +#> "\\n") #> if (plot) { #> outtimes_plot = seq(min(observed$time), max(observed$time), #> length.out = 100) @@ -447,8 +447,8 @@ #> } #> return(mC) #> } -#> <bytecode: 0x5554250> -#> <environment: 0x4eb4b18> +#> <bytecode: 0x560110508c60> +#> <environment: 0x56010f8d8c30> #> #> $cost_notrans #> function (P) @@ -470,8 +470,8 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <bytecode: 0x5073868> -#> <environment: 0x4eb4b18> +#> <bytecode: 0x56010fede550> +#> <environment: 0x56010f8d8c30> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -534,7 +534,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri May 5 12:44:53 2017" +#> [1] "Sat Jul 29 15:14:04 2017" #> #> attr(,"class") #> [1] "mkinfit" "modFit" diff --git a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html index 703dc472..d79aaff6 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -132,7 +132,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html index eec595f0..e0da5a8d 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -131,7 +131,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html index c2a90311..720073f2 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -132,7 +132,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html index 24070b9c..b12abf8c 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -130,7 +130,7 @@ in this fit.

    Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 93901bfa..65bc572a 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -123,7 +123,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/FOMC.solution-2.png b/docs/reference/FOMC.solution-2.png index 0efe8f07..a673bc0e 100644 Binary files a/docs/reference/FOMC.solution-2.png and b/docs/reference/FOMC.solution-2.png differ diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 67a37b4f..9af30b7a 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -152,7 +152,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Gustafson DI and Holden LR (1990) Nonlinear pesticide dissipation in soil: A new model based on spatial variability. Environmental Science and Technology 24, 1032-1038

    diff --git a/docs/reference/HS.solution-2.png b/docs/reference/HS.solution-2.png index 0bdb37a9..2e516447 100644 Binary files a/docs/reference/HS.solution-2.png and b/docs/reference/HS.solution-2.png differ diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 3d608a2f..8f6bbbe2 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -147,7 +147,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/IORE.solution-2.png b/docs/reference/IORE.solution-2.png index df268b64..a83d49c7 100644 Binary files a/docs/reference/IORE.solution-2.png and b/docs/reference/IORE.solution-2.png differ diff --git a/docs/reference/SFO.solution-2.png b/docs/reference/SFO.solution-2.png index 78c083c3..9626091f 100644 Binary files a/docs/reference/SFO.solution-2.png and b/docs/reference/SFO.solution-2.png differ diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 08928135..ef9b8eb7 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -136,7 +136,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/SFORB.solution-2.png b/docs/reference/SFORB.solution-2.png index 9625debf..63a50bf9 100644 Binary files a/docs/reference/SFORB.solution-2.png and b/docs/reference/SFORB.solution-2.png differ diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 112e157d..ebe67733 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -149,7 +149,7 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

    + http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

    Examples

    diff --git a/docs/reference/add_err-4.png b/docs/reference/add_err-4.png index f3d04134..8bbd1758 100644 Binary files a/docs/reference/add_err-4.png and b/docs/reference/add_err-4.png differ diff --git a/docs/reference/add_err-6.png b/docs/reference/add_err-6.png index 05b27247..2a4fe33f 100644 Binary files a/docs/reference/add_err-6.png and b/docs/reference/add_err-6.png differ diff --git a/docs/reference/add_err-8.png b/docs/reference/add_err-8.png index b0182d2a..49c4a5f0 100644 Binary files a/docs/reference/add_err-8.png and b/docs/reference/add_err-8.png differ diff --git a/docs/reference/index.html b/docs/reference/index.html index 2d58eeeb..bf7cd233 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -102,7 +102,7 @@

    Reference - version 0.9.45.2 + version 0.9.46

    diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index 9a681191..0111deb3 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -135,10 +135,10 @@ phenol = list(type = "SFO", to = "anisole"), anisole = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
fit.1 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), quiet = TRUE) - summary(fit.1, data = FALSE)
#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:02 2017 -#> Date of summary: Fri May 5 12:45:02 2017 + summary(fit.1, data = FALSE)
#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:14 2017 +#> Date of summary: Sat Jul 29 15:14:14 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -148,7 +148,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 612 model solutions performed in 3.576 s +#> Fitted with method Port using 612 model solutions performed in 3.558 s #> #> Weighting: none #> @@ -225,10 +225,10 @@ fit.2 <- mkinfit(SFO_SFO_SFO, subset(mccall81_245T, soil == "Commerce"), parms.ini = c(k_phenol_sink = 0), fixed_parms = "k_phenol_sink", quiet = TRUE) - summary(fit.2, data = FALSE)
#> mkin version: 0.9.45.2 -#> R version: 3.4.0 -#> Date of fit: Fri May 5 12:45:04 2017 -#> Date of summary: Fri May 5 12:45:04 2017 + summary(fit.2, data = FALSE)
#> mkin version: 0.9.46 +#> R version: 3.4.1 +#> Date of fit: Sat Jul 29 15:14:15 2017 +#> Date of summary: Sat Jul 29 15:14:15 2017 #> #> Equations: #> d_T245/dt = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -238,7 +238,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.461 s +#> Fitted with method Port using 246 model solutions performed in 1.431 s #> #> Weighting: none #> diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 678750cd..67b7a35e 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -146,7 +146,7 @@ chi-squared test as defined in the FOCUS kinetics report from 2006.

Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

+ http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Examples

diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index 875bd1dd..cdf7c7ef 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -377,17 +377,17 @@

Examples

# Use shorthand notation for parent only degradation
 fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE)
-summary(fit)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:06 2017 
-#> Date of summary: Fri May  5 12:45:06 2017 
+summary(fit)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:18 2017 
+#> Date of summary: Sat Jul 29 15:14:18 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - (alpha/beta) * 1/((time/beta) + 1) * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 64 model solutions performed in 0.206 s
+#> Fitted with method Port using 64 model solutions performed in 0.141 s
 #> 
 #> Weighting: none
 #> 
@@ -456,7 +456,7 @@
   m1 = mkinsub("SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D,
                            solution_type = "eigen", quiet = TRUE)))
#>    user  system elapsed 
-#>   0.912   0.000   0.915 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.888   0.000   0.890 
coef(fit)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -535,7 +535,7 @@
 #> Model cost at call  153 :  371.2134 
 #> Optimisation by method Port successfully terminated.
 #>    user  system elapsed 
-#>   0.792   0.000   0.793 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
+#>   0.728   0.000   0.729 
coef(fit.deSolve)
#>          parent_0 log_k_parent_sink   log_k_parent_m1     log_k_m1_sink 
 #>          99.59848          -3.03822          -2.98030          -5.24750 
endpoints(fit.deSolve)
#> $ff
 #> parent_sink   parent_m1     m1_sink 
 #>    0.485524    0.514476    1.000000 
@@ -576,10 +576,10 @@
 # Weighted fits, including IRLS
 SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", "m1"),
                       m1 = mkinsub("SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.
f.noweight <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(f.noweight)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:17 2017 
-#> Date of summary: Fri May  5 12:45:17 2017 
+summary(f.noweight)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:28 2017 
+#> Date of summary: Sat Jul 29 15:14:28 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -697,10 +697,10 @@
 #>   100       m1    33.13 3.198e+01  1.148e+00
 #>   120       m1    25.15 2.879e+01 -3.640e+00
 #>   120       m1    33.31 2.879e+01  4.520e+00
f.irls <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, reweight.method = "obs", quiet = TRUE)
-summary(f.irls)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:19 2017 
-#> Date of summary: Fri May  5 12:45:19 2017 
+summary(f.irls)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:30 2017 
+#> Date of summary: Sat Jul 29 15:14:30 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -708,7 +708,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 468 model solutions performed in 1.925 s
+#> Fitted with method Port using 468 model solutions performed in 1.914 s
 #> 
 #> Weighting: none then iterative reweighting method obs
 #> 
@@ -818,10 +818,10 @@
 #>   100       m1    33.13 3.199e+01  1.140e+00 2.722
 #>   120       m1    25.15 2.881e+01 -3.659e+00 2.722
 #>   120       m1    33.31 2.881e+01  4.501e+00 2.722
f.w.mean <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, weight = "mean", quiet = TRUE)
-summary(f.w.mean)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:20 2017 
-#> Date of summary: Fri May  5 12:45:20 2017 
+summary(f.w.mean)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:31 2017 
+#> Date of summary: Sat Jul 29 15:14:31 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -829,7 +829,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 155 model solutions performed in 0.699 s
+#> Fitted with method Port using 155 model solutions performed in 0.692 s
 #> 
 #> Weighting: mean
 #> 
@@ -940,10 +940,10 @@
 #>   120       m1    25.15 28.824128  -3.674128
 #>   120       m1    33.31 28.824128   4.485872
f.w.value <- mkinfit(SFO_SFO.ff, subset(FOCUS_2006_D, value != 0), err = "value",
                      quiet = TRUE)
-summary(f.w.value)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:21 2017 
-#> Date of summary: Fri May  5 12:45:21 2017 
+summary(f.w.value)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:32 2017 
+#> Date of summary: Sat Jul 29 15:14:32 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -951,7 +951,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 174 model solutions performed in 0.767 s
+#> Fitted with method Port using 174 model solutions performed in 0.701 s
 #> 
 #> Weighting: manual
 #> 
@@ -1062,10 +1062,10 @@
 errors <- c(parent = 2, m1 = 1)
 dw$err.man <- errors[FOCUS_2006_D$name]
 f.w.man <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE)
-summary(f.w.man)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:22 2017 
-#> Date of summary: Fri May  5 12:45:22 2017 
+summary(f.w.man)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:33 2017 
+#> Date of summary: Sat Jul 29 15:14:33 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1073,7 +1073,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 297 model solutions performed in 1.276 s
+#> Fitted with method Port using 297 model solutions performed in 1.223 s
 #> 
 #> Weighting: manual
 #> 
@@ -1184,10 +1184,10 @@
 #>   120       m1    25.15 28.760616  -3.610616   2
 #>   120       m1    33.31 28.760616   4.549384   2
f.w.man.irls <- mkinfit(SFO_SFO.ff, dw, err = "err.man", quiet = TRUE,
                        reweight.method = "obs")
-summary(f.w.man.irls)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:45:25 2017 
-#> Date of summary: Fri May  5 12:45:25 2017 
+summary(f.w.man.irls)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:14:36 2017 
+#> Date of summary: Sat Jul 29 15:14:36 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -1195,7 +1195,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 628 model solutions performed in 2.626 s
+#> Fitted with method Port using 628 model solutions performed in 2.578 s
 #> 
 #> Weighting: manual then iterative reweighting method obs
 #> 
diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html
index de9815d4..5703b188 100644
--- a/docs/reference/mkinmod.html
+++ b/docs/reference/mkinmod.html
@@ -182,7 +182,7 @@
   Degradation Kinetics from Environmental Fate Studies on Pesticides in EU
   Registration” Report of the FOCUS Work Group on Degradation Kinetics,
   EC Document Reference Sanco/10058/2005 version 2.0, 434 pp,
-  http://esdac.jrc.europa.eu/projects/degradation-kinetics

+  http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

 
NAFTA Technical Working Group on Pesticides (not dated) Guidance for
   Evaluating and Calculating Degradation Kinetics in Environmental 
   Media

@@ -205,7 +205,7 @@
 SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
   m1 = mkinsub("SFO"), verbose = TRUE)
#> Compilation argument:
-#>  /usr/lib/R/bin/R CMD SHLIB file70ea30edf42a.c 2> file70ea30edf42a.c.err.txt 
+#>  /usr/lib/R/bin/R CMD SHLIB file519167a14b3a.c 2> file519167a14b3a.c.err.txt 
 #> Program source:
 #>   1: #include <R.h>
 #>   2: 
diff --git a/docs/reference/mkinparplot-4.png b/docs/reference/mkinparplot-4.png
index 8b32f554..c9f4aadb 100644
Binary files a/docs/reference/mkinparplot-4.png and b/docs/reference/mkinparplot-4.png differ
diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html
index 327a7d8d..b3453e6c 100644
--- a/docs/reference/mkinpredict.html
+++ b/docs/reference/mkinpredict.html
@@ -299,17 +299,17 @@
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "eigen")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.004   0.000   0.004 
  system.time(
+#>   0.004   0.000   0.003 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve")[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.004   0.000   0.002 
  system.time(
+#>   0.000   0.000   0.001 
  system.time(
     print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01),
                 c(parent = 100, m1 = 0), seq(0, 20, by = 0.1),
                 solution_type = "deSolve", use_compiled = FALSE)[201,]))
#>     time   parent       m1
 #> 201   20 4.978707 27.46227
#>    user  system elapsed 
-#>   0.032   0.000   0.033
+#> 0.032 0.000 0.032
#> Warning: Optimisation by method Port did not converge. #> Convergence code is 1
time_default
#> user system elapsed -#> 16.092 0.132 11.761
time_1
#> user system elapsed -#> 25.004 0.000 25.000
+#> 15.992 0.188 11.440
time_1
#> user system elapsed +#> 24.576 0.000 24.578
endpoints(fits.0[["SFO_lin", 2]])
#> $ff #> parent_M1 parent_sink M1_M2 M1_sink #> 0.7340479 0.2659521 0.7505687 0.2494313 diff --git a/docs/reference/plot.mkinfit-10.png b/docs/reference/plot.mkinfit-10.png index 09bb687c..87d3351d 100644 Binary files a/docs/reference/plot.mkinfit-10.png and b/docs/reference/plot.mkinfit-10.png differ diff --git a/docs/reference/plot.mkinfit-4.png b/docs/reference/plot.mkinfit-4.png index 1e90d789..cb52d4ac 100644 Binary files a/docs/reference/plot.mkinfit-4.png and b/docs/reference/plot.mkinfit-4.png differ diff --git a/docs/reference/plot.mkinfit-6.png b/docs/reference/plot.mkinfit-6.png index 1dfbbe4c..8e0faa21 100644 Binary files a/docs/reference/plot.mkinfit-6.png and b/docs/reference/plot.mkinfit-6.png differ diff --git a/docs/reference/plot.mkinfit-8.png b/docs/reference/plot.mkinfit-8.png index e4ab674a..129f1445 100644 Binary files a/docs/reference/plot.mkinfit-8.png and b/docs/reference/plot.mkinfit-8.png differ diff --git a/docs/reference/plot.mmkin-2.png b/docs/reference/plot.mmkin-2.png index a26e413f..7739e3b0 100644 Binary files a/docs/reference/plot.mmkin-2.png and b/docs/reference/plot.mmkin-2.png differ diff --git a/docs/reference/plot.mmkin-4.png b/docs/reference/plot.mmkin-4.png index f23ed172..e2eb3aae 100644 Binary files a/docs/reference/plot.mmkin-4.png and b/docs/reference/plot.mmkin-4.png differ diff --git a/docs/reference/plot.mmkin-6.png b/docs/reference/plot.mmkin-6.png index dc24d92f..3bbd390a 100644 Binary files a/docs/reference/plot.mmkin-6.png and b/docs/reference/plot.mmkin-6.png differ diff --git a/docs/reference/schaefer07_complex_case-4.png b/docs/reference/schaefer07_complex_case-4.png index b87ccb82..b90185a1 100644 Binary files a/docs/reference/schaefer07_complex_case-4.png and b/docs/reference/schaefer07_complex_case-4.png differ diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index dbed926d..f20e3948 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -177,21 +177,21 @@ Degradation Kinetics from Environmental Fate Studies on Pesticides in EU Registration” Report of the FOCUS Work Group on Degradation Kinetics, EC Document Reference Sanco/10058/2005 version 2.0, 434 pp, - http://esdac.jrc.europa.eu/projects/degradation-kinetics

+ http://esdac.jrc.ec.europa.eu/projects/degradation-kinetics

Examples

- 
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:46:20 2017 
-#> Date of summary: Fri May  5 12:46:20 2017 
+    
  summary(mkinfit(mkinmod(parent = mkinsub("SFO")), FOCUS_2006_A, quiet = TRUE))
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:15:30 2017 
+#> Date of summary: Sat Jul 29 15:15:30 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent
 #> 
 #> Model predictions using solution type analytical 
 #> 
-#> Fitted with method Port using 35 model solutions performed in 0.082 s
+#> Fitted with method Port using 35 model solutions performed in 0.084 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html
index d8ff3a1e..173af92e 100644
--- a/docs/reference/synthetic_data_for_UBA.html
+++ b/docs/reference/synthetic_data_for_UBA.html
@@ -156,10 +156,10 @@
                             M1 = list(type = "SFO"),
                             M2 = list(type = "SFO"), use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 fit <- mkinfit(m_synth_SFO_lin, synthetic_data_for_UBA_2014[[1]]$data, quiet = TRUE)
-plot_sep(fit)
summary(fit)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:46:23 2017 
-#> Date of summary: Fri May  5 12:46:23 2017 
+plot_sep(fit)
summary(fit)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:15:33 2017 
+#> Date of summary: Sat Jul 29 15:15:34 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -168,7 +168,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 381 model solutions performed in 2.203 s
+#> Fitted with method Port using 381 model solutions performed in 2.241 s
 #> 
 #> Weighting: none
 #> 
diff --git a/docs/reference/synthetic_data_for_UBA_2014-10.png b/docs/reference/synthetic_data_for_UBA_2014-10.png
index b98940ff..7e15e1b3 100644
Binary files a/docs/reference/synthetic_data_for_UBA_2014-10.png and b/docs/reference/synthetic_data_for_UBA_2014-10.png differ
diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html
index c14740c2..bbf15a41 100644
--- a/docs/reference/transform_odeparms.html
+++ b/docs/reference/transform_odeparms.html
@@ -170,10 +170,10 @@
   parent = list(type = "SFO", to = "m1", sink = TRUE),
   m1 = list(type = "SFO"))
#> Successfully compiled differential equation model from auto-generated C code.
# Fit the model to the FOCUS example dataset D using defaults
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
-summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:46:24 2017 
-#> Date of summary: Fri May  5 12:46:24 2017 
+summary(fit, data=FALSE) # See transformed and backtransformed parameters
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:15:35 2017 
+#> Date of summary: Sat Jul 29 15:15:35 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -181,7 +181,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 153 model solutions performed in 0.61 s
+#> Fitted with method Port using 153 model solutions performed in 0.608 s
 #> 
 #> Weighting: none
 #> 
@@ -247,10 +247,10 @@
 #> m1     131.761 437.70

 
 fit.2 <- mkinfit(SFO_SFO, FOCUS_2006_D, transform_rates = FALSE, quiet = TRUE)
-summary(fit.2, data=FALSE)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:46:26 2017 
-#> Date of summary: Fri May  5 12:46:26 2017 
+summary(fit.2, data=FALSE)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:15:36 2017 
+#> Date of summary: Sat Jul 29 15:15:36 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent_sink * parent - k_parent_m1 * parent
@@ -258,7 +258,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 352 model solutions performed in 1.437 s
+#> Fitted with method Port using 352 model solutions performed in 1.401 s
 #> 
 #> Weighting: none
 #> 
@@ -337,10 +337,10 @@
   m1 = list(type = "SFO"),
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 fit.ff <- mkinfit(SFO_SFO.ff, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff, data = FALSE)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:46:27 2017 
-#> Date of summary: Fri May  5 12:46:27 2017 
+summary(fit.ff, data = FALSE)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:15:37 2017 
+#> Date of summary: Sat Jul 29 15:15:37 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -348,7 +348,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 185 model solutions performed in 0.776 s
+#> Fitted with method Port using 185 model solutions performed in 0.772 s
 #> 
 #> Weighting: none
 #> 
@@ -421,10 +421,10 @@
   use_of_ff = "max")
#> Successfully compiled differential equation model from auto-generated C code.

 
 fit.ff.2 <- mkinfit(SFO_SFO.ff.2, FOCUS_2006_D, quiet = TRUE)
-summary(fit.ff.2, data = FALSE)
#> mkin version:    0.9.45.2 
-#> R version:       3.4.0 
-#> Date of fit:     Fri May  5 12:46:28 2017 
-#> Date of summary: Fri May  5 12:46:28 2017 
+summary(fit.ff.2, data = FALSE)
#> mkin version:    0.9.46 
+#> R version:       3.4.1 
+#> Date of fit:     Sat Jul 29 15:15:38 2017 
+#> Date of summary: Sat Jul 29 15:15:38 2017 
 #> 
 #> Equations:
 #> d_parent/dt = - k_parent * parent
@@ -432,7 +432,7 @@
 #> 
 #> Model predictions using solution type deSolve 
 #> 
-#> Fitted with method Port using 104 model solutions performed in 0.433 s
+#> Fitted with method Port using 104 model solutions performed in 0.416 s
 #> 
 #> Weighting: none
 #> 
-- 
cgit v1.2.1