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a/docs/articles/FOCUS_D.html b/docs/articles/FOCUS_D.html index f32d7f82..1c4edbd0 100644 --- a/docs/articles/FOCUS_D.html +++ b/docs/articles/FOCUS_D.html @@ -24,7 +24,13 @@
  • News
  • - + @@ -110,8 +116,8 @@
    summary(fit)
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Wed Nov  2 16:25:22 2016 
    -## Date of summary: Wed Nov  2 16:25:22 2016 
    +## Date of fit:     Fri Nov  4 16:56:20 2016 
    +## Date of summary: Fri Nov  4 16:56:20 2016 
     ## 
     ## Equations:
     ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
    @@ -119,7 +125,7 @@
     ## 
     ## Model predictions using solution type deSolve 
     ## 
    -## Fitted with method Port using 153 model solutions performed in 0.665 s
    +## Fitted with method Port using 153 model solutions performed in 0.661 s
     ## 
     ## Weighting: none
     ## 
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    index 6a9c6ba5..2244a359 100644
    --- a/docs/articles/FOCUS_L.html
    +++ b/docs/articles/FOCUS_L.html
    @@ -24,7 +24,13 @@
     
  • News
  • - + @@ -57,15 +63,15 @@ FOCUS_2006_L1_mkin <- summary(m.L1.SFO)
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Fri Nov  4 15:38:03 2016 
    -## Date of summary: Fri Nov  4 15:38:03 2016 
    +## Date of fit:     Fri Nov  4 16:56:21 2016 
    +## Date of summary: Fri Nov  4 16:56:21 2016 
     ## 
     ## Equations:
     ## d_parent = - k_parent_sink * parent
     ## 
     ## Model predictions using solution type analytical 
     ## 
    -## Fitted with method Port using 37 model solutions performed in 0.089 s
    +## Fitted with method Port using 37 model solutions performed in 0.087 s
     ## 
     ## Weighting: none
     ## 
    @@ -150,8 +156,8 @@ FOCUS_2006_L1_mkin <- 
    summary(m.L1.FOMC, data = FALSE)
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Fri Nov  4 15:38:04 2016 
    -## Date of summary: Fri Nov  4 15:38:04 2016 
    +## Date of fit:     Fri Nov  4 16:56:21 2016 
    +## Date of summary: Fri Nov  4 16:56:21 2016 
     ## 
     ## 
     ## Warning: Optimisation by method Port did not converge.
    @@ -163,7 +169,7 @@ FOCUS_2006_L1_mkin <-  
    summary(m.L2.FOMC, data = FALSE)
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Fri Nov  4 15:38:05 2016 
    -## Date of summary: Fri Nov  4 15:38:05 2016 
    +## Date of fit:     Fri Nov  4 16:56:22 2016 
    +## Date of summary: Fri Nov  4 16:56:22 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 0.19 s
    +## Fitted with method Port using 81 model solutions performed in 0.199 s
     ## 
     ## Weighting: none
     ## 
    @@ -317,8 +323,8 @@ FOCUS_2006_L2_mkin <- 
    summary(m.L2.DFOP, data = FALSE)
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Fri Nov  4 15:38:06 2016 
    -## Date of summary: Fri Nov  4 15:38:06 2016 
    +## Date of fit:     Fri Nov  4 16:56:23 2016 
    +## Date of summary: Fri Nov  4 16:56:23 2016 
     ## 
     ## Equations:
     ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
    @@ -327,7 +333,7 @@ FOCUS_2006_L2_mkin <-  
    summary(mm.L3[["DFOP", 1]])
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Fri Nov  4 15:38:07 2016 
    -## Date of summary: Fri Nov  4 15:38:07 2016 
    +## Date of fit:     Fri Nov  4 16:56:24 2016 
    +## Date of summary: Fri Nov  4 16:56:25 2016 
     ## 
     ## Equations:
     ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
    @@ -416,7 +422,7 @@ mm.L3 <-  
    summary(mm.L4[["SFO", 1]], data = FALSE)
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Fri Nov  4 15:38:07 2016 
    -## Date of summary: Fri Nov  4 15:38:08 2016 
    +## Date of fit:     Fri Nov  4 16:56:25 2016 
    +## Date of summary: Fri Nov  4 16:56:25 2016 
     ## 
     ## Equations:
     ## d_parent = - k_parent_sink * parent
     ## 
     ## Model predictions using solution type analytical 
     ## 
    -## Fitted with method Port using 46 model solutions performed in 0.112 s
    +## Fitted with method Port using 46 model solutions performed in 0.109 s
     ## 
     ## Weighting: none
     ## 
    @@ -566,15 +572,15 @@ mm.L4 <- 
    summary(mm.L4[["FOMC", 1]], data = FALSE)
    ## mkin version:    0.9.44.9000 
     ## R version:       3.3.2 
    -## Date of fit:     Fri Nov  4 15:38:08 2016 
    -## Date of summary: Fri Nov  4 15:38:08 2016 
    +## Date of fit:     Fri Nov  4 16:56:25 2016 
    +## Date of summary: Fri Nov  4 16:56:25 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 0.148 s
    +## Fitted with method Port using 66 model solutions performed in 0.16 s
     ## 
     ## Weighting: none
     ## 
    diff --git a/docs/articles/FOCUS_L_cache/html/__packages b/docs/articles/FOCUS_L_cache/html/__packages
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    --- a/docs/articles/FOCUS_L_cache/html/__packages
    +++ /dev/null
    @@ -1,8 +0,0 @@
    -base
    -minpack.lm
    -rootSolve
    -inline
    -mkin
    -knitr
    -microbenchmark
    -ggplot2
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    index 09039f62..e1572b17 100644
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    +++ b/docs/articles/compiled_models.html
    @@ -24,7 +24,13 @@
     
  • News
  • - + @@ -72,21 +78,21 @@ mb.1 <- micr print(mb.1)
    ## Unit: milliseconds
     ##                   expr       min        lq      mean    median        uq
    -##  deSolve, not compiled 6581.1731 6598.7831 6630.0395 6616.3931 6654.4726
    -##       Eigenvalue based  880.1617  890.3517  911.2758  900.5416  926.8328
    -##      deSolve, compiled  739.4343  749.6078  753.6543  759.7813  760.7643
    +##  deSolve, not compiled 6326.4518 6378.7429 6476.2219 6431.0341 6551.1069
    +##       Eigenvalue based  925.7797  935.9924  939.8725  946.2051  946.9189
    +##      deSolve, compiled  740.2821  750.0017  767.8440  759.7212  781.6249
     ##        max neval cld
    -##  6692.5522     3   c
    -##   953.1240     3  b 
    -##   761.7474     3 a
    +## 6671.1797 3 b +## 947.6327 3 a +## 803.5287 3 a
    autoplot(mb.1)

    -

    We see that using the compiled model is by a factor of 8.7 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

    +

    We see that using the compiled model is by a factor of 8.5 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 8.708286
    -## Eigenvalue based      1.185264
    +## deSolve, not compiled 8.464993
    +## Eigenvalue based      1.245464
     ## deSolve, compiled     1.000000
    @@ -108,18 +114,18 @@ smb.1["median"]/smbprint(mb.2)
    ## Unit: seconds
     ##                   expr       min        lq      mean    median        uq
    -##  deSolve, not compiled 13.756286 13.813205 13.874083 13.870125 13.932982
    -##      deSolve, compiled  1.323196  1.372916  1.391915  1.422635  1.426274
    +##  deSolve, not compiled 13.619556 13.761382 13.825679 13.903207 13.928741
    +##      deSolve, compiled  1.316871  1.322577  1.358847  1.328283  1.379834
     ##        max neval cld
    -##  13.995838     3   b
    -##   1.429913     3  a
    +## 13.954275 3 b +## 1.431386 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 9.7 using the version of the differential equation model compiled from C code!

    +

    Here we get a performance benefit of a factor of 10.5 using the version of the differential equation model compiled from C code!

    This vignette was built with mkin 0.9.44.9000 on

    ## R version 3.3.2 (2016-10-31)
     ## Platform: x86_64-pc-linux-gnu (64-bit)
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  • News
  • - + diff --git a/docs/articles/mkin_cache/html/__packages b/docs/articles/mkin_cache/html/__packages index 03ece635..c8b1e877 100644 --- a/docs/articles/mkin_cache/html/__packages +++ b/docs/articles/mkin_cache/html/__packages @@ -1,13 +1,8 @@ base -datasets -utils -grDevices -graphics -stats knitr minpack.lm rootSolve -methods inline -parallel mkin +microbenchmark +ggplot2 diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData deleted file mode 100644 index d11ccf31..00000000 Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.RData and /dev/null differ diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb deleted file mode 100644 index 5ac4f484..00000000 Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdb and /dev/null differ diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx deleted file mode 100644 index 8983f69e..00000000 Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_60bc93a2c97228ef4815e972498edefa.rdx and /dev/null differ diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData index 8fd3567d..e52d9b7b 100644 Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData and b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.RData differ diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb index 7f4d6c92..ff7ed49e 100644 Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb and b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdb differ diff --git a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx index 7f5f16b7..7ec72c33 100644 Binary files a/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx and b/docs/articles/mkin_cache/html/unnamed-chunk-2_f17bce9fa804585d9877abdce3dac24a.rdx differ diff --git a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png index 2e7e2244..d34e3805 100644 Binary files a/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png and b/docs/articles/mkin_files/figure-html/unnamed-chunk-2-1.png differ diff --git a/docs/news/index.html b/docs/news/index.html index 7c9b63f7..dc316b7a 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -60,7 +60,12 @@ diff --git a/docs/reference/DFOP.solution.html b/docs/reference/DFOP.solution.html index 7d036804..c0690f41 100644 --- a/docs/reference/DFOP.solution.html +++ b/docs/reference/DFOP.solution.html @@ -6,8 +6,7 @@ - - — DFOP.solution • mkin +Double First-Order in Parallel kinetics — DFOP.solution • mkin @@ -61,7 +60,12 @@ @@ -73,8 +77,7 @@
    diff --git a/docs/reference/Extract.mmkin.html b/docs/reference/Extract.mmkin.html index cfe6329b..ad4614fb 100644 --- a/docs/reference/Extract.mmkin.html +++ b/docs/reference/Extract.mmkin.html @@ -60,7 +60,12 @@
    @@ -188,7 +193,7 @@ #> #> $time #> user system elapsed -#> 0.316 0.000 0.317 +#> 0.264 0.000 0.262 #> #> $mkinmod #> <mkinmod> model generated with @@ -374,7 +379,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $cost_notrans #> function (P) @@ -396,7 +401,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d4a3b0> +#> <environment: 0x50d32d0> #> #> $hessian_notrans #> parent_0 alpha beta @@ -462,7 +467,7 @@ #> 99.66619 #> #> $date -#> [1] "Fri Nov 4 15:36:31 2016" +#> [1] "Fri Nov 4 17:08:52 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit"
    fits["SFO", "B"]
    #> dataset @@ -541,7 +546,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -728,7 +733,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -750,7 +755,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -813,7 +818,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 2016" #> #> attr(,"class") #> [1] "mkinfit" "modFit"
    fits["SFO", "B", drop = TRUE]
    #> [[1]] @@ -889,7 +894,7 @@ #> #> $time #> user system elapsed -#> 0.076 0.000 0.077 +#> 0.068 0.000 0.067 #> #> $mkinmod #> <mkinmod> model generated with @@ -1076,7 +1081,7 @@ #> } #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $cost_notrans #> function (P) @@ -1098,7 +1103,7 @@ #> scaleVar = scaleVar) #> return(mC) #> } -#> <environment: 0x5d98970> +#> <environment: 0x4f17408> #> #> $hessian_notrans #> parent_0 k_parent_sink @@ -1161,7 +1166,7 @@ #> 99.17407 #> #> $date -#> [1] "Fri Nov 4 15:36:30 2016" +#> [1] "Fri Nov 4 17:08:51 2016" #> #> 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 97af2f9c..13dfa186 100644 --- a/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html +++ b/docs/reference/FOCUS_2006_DFOP_ref_A_to_B.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_DFOP_ref_A_to_B • mkin +Results of fitting the DFOP model to Datasets A to B of FOCUS (2006) — FOCUS_2006_DFOP_ref_A_to_B • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    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 1487e2c9..5b36ac74 100644 --- a/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_FOMC_ref_A_to_F.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_FOMC_ref_A_to_F • mkin +Results of fitting the FOMC model to Datasets A to F of FOCUS (2006) — FOCUS_2006_FOMC_ref_A_to_F • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    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 4571c175..446ce4d7 100644 --- a/docs/reference/FOCUS_2006_HS_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_HS_ref_A_to_F.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_HS_ref_A_to_F • mkin +Results of fitting the HS model to Datasets A to F of FOCUS (2006) — FOCUS_2006_HS_ref_A_to_F • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    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 7003fa0e..db462f10 100644 --- a/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html +++ b/docs/reference/FOCUS_2006_SFO_ref_A_to_F.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_SFO_ref_A_to_F • mkin +Results of fitting the SFO model to Datasets A to F of FOCUS (2006) — FOCUS_2006_SFO_ref_A_to_F • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/FOCUS_2006_datasets.html b/docs/reference/FOCUS_2006_datasets.html index 83edd323..ffc7558e 100644 --- a/docs/reference/FOCUS_2006_datasets.html +++ b/docs/reference/FOCUS_2006_datasets.html @@ -6,8 +6,7 @@ - - — FOCUS_2006_datasets • mkin +Datasets A to F from the FOCUS Kinetics report from 2006 — FOCUS_2006_datasets • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/FOMC.solution.html b/docs/reference/FOMC.solution.html index 83bca886..fdbf0d1f 100644 --- a/docs/reference/FOMC.solution.html +++ b/docs/reference/FOMC.solution.html @@ -6,7 +6,7 @@ - First-Order Multi-Compartment kinetics — FOMC.solution • mkin +First-Order Multi-Compartment kinetics — FOMC.solution • mkin @@ -60,7 +60,12 @@
    @@ -72,7 +77,7 @@
    diff --git a/docs/reference/HS.solution.html b/docs/reference/HS.solution.html index 13db29aa..fbe0b590 100644 --- a/docs/reference/HS.solution.html +++ b/docs/reference/HS.solution.html @@ -6,7 +6,7 @@ - Hockey-Stick kinetics — HS.solution • mkin +Hockey-Stick kinetics — HS.solution • mkin @@ -60,7 +60,12 @@
    @@ -72,7 +77,7 @@
    diff --git a/docs/reference/IORE.solution.html b/docs/reference/IORE.solution.html index 56c2b48e..553c38b0 100644 --- a/docs/reference/IORE.solution.html +++ b/docs/reference/IORE.solution.html @@ -6,7 +6,7 @@ - Indeterminate order rate equation kinetics — IORE.solution • mkin +Indeterminate order rate equation kinetics — IORE.solution • mkin @@ -60,7 +60,12 @@
    @@ -72,7 +77,7 @@
    diff --git a/docs/reference/SFO.solution.html b/docs/reference/SFO.solution.html index 8ff5b5ba..2ead8f24 100644 --- a/docs/reference/SFO.solution.html +++ b/docs/reference/SFO.solution.html @@ -6,7 +6,7 @@ - Single First-Order kinetics — SFO.solution • mkin +Single First-Order kinetics — SFO.solution • mkin @@ -60,7 +60,12 @@
    @@ -72,7 +77,7 @@
    diff --git a/docs/reference/SFORB.solution.html b/docs/reference/SFORB.solution.html index 43b6028a..be425d83 100644 --- a/docs/reference/SFORB.solution.html +++ b/docs/reference/SFORB.solution.html @@ -6,7 +6,7 @@ - Single First-Order Reversible Binding kinetics — SFORB.solution • mkin +Single First-Order Reversible Binding kinetics — SFORB.solution • mkin @@ -60,7 +60,12 @@
    @@ -72,7 +77,7 @@
    diff --git a/docs/reference/add_err.html b/docs/reference/add_err.html index 8e491bc9..0a126c5c 100644 --- a/docs/reference/add_err.html +++ b/docs/reference/add_err.html @@ -6,8 +6,7 @@ - - — add_err • mkin +Add normally distributed errors to simulated kinetic degradation data — add_err • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index a3716060..44a8f4c4 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -6,8 +6,7 @@ - - — endpoints • mkin +Function to calculate endpoints for further use from kinetic models fitted with mkinfit — endpoints • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/geometric_mean.html b/docs/reference/geometric_mean.html index 633e0865..97352ff8 100644 --- a/docs/reference/geometric_mean.html +++ b/docs/reference/geometric_mean.html @@ -6,7 +6,7 @@ - Calculate the geometric mean — geometric_mean • mkin +Calculate the geometric mean — geometric_mean • mkin @@ -60,7 +60,12 @@
    @@ -72,7 +77,7 @@
    diff --git a/docs/reference/ilr.html b/docs/reference/ilr.html index 955b5c58..95fed72e 100644 --- a/docs/reference/ilr.html +++ b/docs/reference/ilr.html @@ -6,8 +6,7 @@ - - — ilr • mkin +Function to perform isometric log-ratio transformation — ilr • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/index.html b/docs/reference/index.html index b7d59a21..32455baa 100644 --- a/docs/reference/index.html +++ b/docs/reference/index.html @@ -60,7 +60,12 @@
    diff --git a/docs/reference/mccall81_245T.html b/docs/reference/mccall81_245T.html index d32acb5b..6eb4741b 100644 --- a/docs/reference/mccall81_245T.html +++ b/docs/reference/mccall81_245T.html @@ -6,8 +6,7 @@ - - — mccall81_245T • mkin +Datasets on aerobic soil metabolism of 2,4,5-T in six soils — mccall81_245T • mkin @@ -61,7 +60,12 @@ @@ -73,8 +77,7 @@
    @@ -119,8 +122,8 @@ fixed_parms = "k_phenol_sink", quiet = TRUE) summary(fit.2, data = FALSE)
    #> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:38 2016 -#> Date of summary: Fri Nov 4 15:36:38 2016 +#> Date of fit: Fri Nov 4 17:08:59 2016 +#> Date of summary: Fri Nov 4 17:08:59 2016 #> #> Equations: #> d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -130,7 +133,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 246 model solutions performed in 1.886 s +#> Fitted with method Port using 246 model solutions performed in 1.497 s #> #> Weighting: none #> diff --git a/docs/reference/mkin_long_to_wide.html b/docs/reference/mkin_long_to_wide.html index 21a8a8f8..fa131a6d 100644 --- a/docs/reference/mkin_long_to_wide.html +++ b/docs/reference/mkin_long_to_wide.html @@ -6,8 +6,7 @@ - - — mkin_long_to_wide • mkin +Convert a dataframe from long to wide format — mkin_long_to_wide • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/mkin_wide_to_long.html b/docs/reference/mkin_wide_to_long.html index fe6e47e4..077c0b7d 100644 --- a/docs/reference/mkin_wide_to_long.html +++ b/docs/reference/mkin_wide_to_long.html @@ -6,8 +6,7 @@ - - — mkin_wide_to_long • mkin +Convert a dataframe with observations over time into long format — mkin_wide_to_long • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/mkinds.html b/docs/reference/mkinds.html index f5dd4c88..522aab33 100644 --- a/docs/reference/mkinds.html +++ b/docs/reference/mkinds.html @@ -60,7 +60,12 @@
    diff --git a/docs/reference/mkinerrmin.html b/docs/reference/mkinerrmin.html index 8d420165..d212e3b2 100644 --- a/docs/reference/mkinerrmin.html +++ b/docs/reference/mkinerrmin.html @@ -6,8 +6,7 @@ - - — mkinerrmin • mkin +Calculate the minimum error to assume in order to pass the variance test — mkinerrmin • mkin @@ -61,7 +60,12 @@ @@ -73,8 +77,7 @@
    diff --git a/docs/reference/mkinfit.html b/docs/reference/mkinfit.html index b298d90a..93185eff 100644 --- a/docs/reference/mkinfit.html +++ b/docs/reference/mkinfit.html @@ -6,8 +6,7 @@ - - — mkinfit • mkin +Fit a kinetic model to data with one or more state variables — mkinfit • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    @@ -356,8 +359,8 @@ fit <- mkinfit("FOMC", FOCUS_2006_C, quiet = TRUE) summary(fit)
    #> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:41 2016 -#> Date of summary: Fri Nov 4 15:36:41 2016 +#> Date of fit: Fri Nov 4 17:09:01 2016 +#> Date of summary: Fri Nov 4 17:09:01 2016 #> #> Equations: #> d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent @@ -433,7 +436,7 @@ 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 -#> 1.244 1.208 0.933
    coef(fit)
    #> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink +#> 1.256 1.216 0.946
    coef(fit)
    #> parent_0 log_k_parent_sink log_k_parent_m1 log_k_m1_sink #> 99.59848 -3.03822 -2.98030 -5.24750
    #> $ff #> parent_sink parent_m1 m1_sink #> 0.485524 0.514476 1.000000 diff --git a/docs/reference/mkinmod.html b/docs/reference/mkinmod.html index 7dba1b6d..f328c34a 100644 --- a/docs/reference/mkinmod.html +++ b/docs/reference/mkinmod.html @@ -6,8 +6,7 @@ - - — mkinmod • mkin +Function to set up a kinetic model with one or more state variables — mkinmod • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/mkinparplot.html b/docs/reference/mkinparplot.html index 923abc6d..764f1ab4 100644 --- a/docs/reference/mkinparplot.html +++ b/docs/reference/mkinparplot.html @@ -6,8 +6,8 @@ - - — mkinparplot • mkin +Function to plot the confidence intervals obtained using + list(list("mkinfit")) — mkinparplot • mkin @@ -61,7 +61,12 @@
    @@ -73,8 +78,8 @@
    diff --git a/docs/reference/mkinplot.html b/docs/reference/mkinplot.html index 5fe94a8a..921affdc 100644 --- a/docs/reference/mkinplot.html +++ b/docs/reference/mkinplot.html @@ -6,8 +6,7 @@ - - — mkinplot • mkin +Plot the observed data and the fitted model of an mkinfit object — mkinplot • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/mkinpredict.html b/docs/reference/mkinpredict.html index f7eb950a..9f00dab7 100644 --- a/docs/reference/mkinpredict.html +++ b/docs/reference/mkinpredict.html @@ -6,8 +6,7 @@ - - — mkinpredict • mkin +Produce predictions from a kinetic model using specific parameters — mkinpredict • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    @@ -272,7 +275,7 @@ 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 -#> 0.008 0.024 0.005
    system.time( +#> 0.004 0.028 0.004
    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 @@ -282,7 +285,7 @@ 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 -#> 0.036 0.000 0.037
    +#> 0.052 0.000 0.052
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/mkinsub.html b/docs/reference/mkinsub.html index 8424eaab..8bb2ce1c 100644 --- a/docs/reference/mkinsub.html +++ b/docs/reference/mkinsub.html @@ -6,8 +6,7 @@ - - — mkinsub • mkin +Function to set up a kinetic submodel for one state variable — mkinsub • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/mmkin.html b/docs/reference/mmkin.html index 5613a720..a21a980b 100644 --- a/docs/reference/mmkin.html +++ b/docs/reference/mmkin.html @@ -6,8 +6,7 @@ - - — mmkin • mkin +Fit one or more kinetic models with one or more state variables to one or more datasets — mmkin • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/plot.mkinfit.html b/docs/reference/plot.mkinfit.html index e7158180..52db9bc6 100644 --- a/docs/reference/plot.mkinfit.html +++ b/docs/reference/plot.mkinfit.html @@ -6,8 +6,7 @@ - - — plot.mkinfit • mkin +Plot the observed data and the fitted model of an mkinfit object — plot.mkinfit • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index ef5c04b7..eac31273 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -6,8 +6,7 @@ - - — plot.mmkin • mkin +Plot model fits (observed and fitted) and the residuals for a row or column of an mmkin object — plot.mmkin • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/print.mkinds.html b/docs/reference/print.mkinds.html index c578f4ee..9057114d 100644 --- a/docs/reference/print.mkinds.html +++ b/docs/reference/print.mkinds.html @@ -6,8 +6,7 @@ - - — print.mkinds • mkin +Print mkinds objects — print.mkinds • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/print.mkinmod.html b/docs/reference/print.mkinmod.html index 3f653971..2034ea10 100644 --- a/docs/reference/print.mkinmod.html +++ b/docs/reference/print.mkinmod.html @@ -6,8 +6,7 @@ - - — print.mkinmod • mkin +Print mkinmod objects — print.mkinmod • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/schaefer07_complex_case.html b/docs/reference/schaefer07_complex_case.html index c63ba490..e2f845d9 100644 --- a/docs/reference/schaefer07_complex_case.html +++ b/docs/reference/schaefer07_complex_case.html @@ -6,8 +6,7 @@ - - — schaefer07_complex_case • mkin +Metabolism data set used for checking the software quality of KinGUI — schaefer07_complex_case • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/summary.mkinfit.html b/docs/reference/summary.mkinfit.html index 241964a7..f67bc1d1 100644 --- a/docs/reference/summary.mkinfit.html +++ b/docs/reference/summary.mkinfit.html @@ -6,8 +6,7 @@ - - — summary.mkinfit • mkin +Summary method for class "mkinfit" — summary.mkinfit • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    @@ -139,8 +142,8 @@

    Examples

    summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
    #> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:49 2016 -#> Date of summary: Fri Nov 4 15:36:49 2016 +#> Date of fit: Fri Nov 4 17:09:10 2016 +#> Date of summary: Fri Nov 4 17:09:10 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent diff --git a/docs/reference/synthetic_data_for_UBA.html b/docs/reference/synthetic_data_for_UBA.html index 333b3dbf..c6f29582 100644 --- a/docs/reference/synthetic_data_for_UBA.html +++ b/docs/reference/synthetic_data_for_UBA.html @@ -6,8 +6,7 @@ - - — synthetic_data_for_UBA_2014 • mkin +Synthetic datasets for one parent compound with two metabolites — synthetic_data_for_UBA_2014 • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    diff --git a/docs/reference/transform_odeparms.html b/docs/reference/transform_odeparms.html index 5ee1e9cc..60208ff4 100644 --- a/docs/reference/transform_odeparms.html +++ b/docs/reference/transform_odeparms.html @@ -6,8 +6,7 @@ - - — transform_odeparms • mkin +Functions to transform and backtransform kinetic parameters for fitting — transform_odeparms • mkin @@ -61,7 +60,12 @@
    @@ -73,8 +77,7 @@
    @@ -146,8 +149,8 @@ fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE) summary(fit, data=FALSE) # See transformed and backtransformed parameters
    #> mkin version: 0.9.44.9000 #> R version: 3.3.2 -#> Date of fit: Fri Nov 4 15:36:50 2016 -#> Date of summary: Fri Nov 4 15:36:50 2016 +#> Date of fit: Fri Nov 4 17:09:11 2016 +#> Date of summary: Fri Nov 4 17:09:11 2016 #> #> Equations: #> d_parent = - k_parent_sink * parent - k_parent_m1 * parent @@ -155,7 +158,7 @@ #> #> Model predictions using solution type deSolve #> -#> Fitted with method Port using 153 model solutions performed in 0.663 s +#> Fitted with method Port using 153 model solutions performed in 0.638 s #> #> Weighting: none #> diff --git a/docs/reference/unknown-10.png b/docs/reference/unknown-10.png deleted file mode 100644 index 09bb687c..00000000 Binary files a/docs/reference/unknown-10.png and /dev/null differ diff --git a/docs/reference/unknown-2.png b/docs/reference/unknown-2.png deleted file mode 100644 index a26e413f..00000000 Binary files a/docs/reference/unknown-2.png and /dev/null differ diff --git a/docs/reference/unknown-4.png b/docs/reference/unknown-4.png deleted file mode 100644 index f23ed172..00000000 Binary files a/docs/reference/unknown-4.png and /dev/null differ diff --git a/docs/reference/unknown-6.png b/docs/reference/unknown-6.png deleted file mode 100644 index dc24d92f..00000000 Binary files a/docs/reference/unknown-6.png and /dev/null differ diff --git a/docs/reference/unknown-8.png b/docs/reference/unknown-8.png deleted file mode 100644 index e4ab674a..00000000 Binary files a/docs/reference/unknown-8.png and /dev/null differ -- cgit v1.2.1