mkin

The R package mkin provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as needed for modelling the formation and decline of transformation products, or if several compartments are involved.

Installation

diff --git a/README.md b/README.md index ca06b9b1..e40aad6a 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # mkin -[![](http://www.r-pkg.org/badges/version/mkin)](https://cran.rstudio.com/web/packages/mkin/index.html) +[![](http://www.r-pkg.org/badges/version/mkin)](http://cran.r-project.org/package=mkin) The R package **mkin** provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as diff --git a/inst/web/DFOP.solution.html b/inst/web/DFOP.solution.html index fb73ffb8..4746beef 100644 --- a/inst/web/DFOP.solution.html +++ b/inst/web/DFOP.solution.html @@ -2,7 +2,7 @@ -DFOP.solution. mkin 0.9.42 +DFOP.solution. mkin 0.9.43 @@ -32,7 +32,7 @@

- mkin 0.9.42 + mkin 0.9.43

Index

[.mmkin. mkin 0.9.42

[.mmkin. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.42

FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.42

FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

FOCUS_2006_HS_ref_A_to_F. mkin 0.9.42

FOCUS_2006_HS_ref_A_to_F. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.42

FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

FOCUS_2006_datasets. mkin 0.9.42

FOCUS_2006_datasets. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

FOMC.solution. mkin 0.9.42

FOMC.solution. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

HS.solution. mkin 0.9.42

HS.solution. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

IORE.solution. mkin 0.9.42

IORE.solution. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

SFO.solution. mkin 0.9.42

SFO.solution. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

SFORB.solution. mkin 0.9.42

SFORB.solution. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

endpoints. mkin 0.9.42

endpoints. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

geometric_mean. mkin 0.9.42

geometric_mean. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

ilr. mkin 0.9.42

ilr. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mccall81_245T. mkin 0.9.42

mccall81_245T. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkin version: 0.9.42 +

mkin version: 0.9.43 R version: 3.2.4 -Date of fit: Wed Mar 23 18:10:44 2016 -Date of summary: Wed Mar 23 18:10:44 2016 +Date of fit: Thu Mar 24 08:26:26 2016 +Date of summary: Thu Mar 24 08:26:26 2016 Equations: d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -124,7 +124,7 @@ d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole Model predictions using solution type deSolve -Fitted with method Port using 246 model solutions performed in 1.482 s +Fitted with method Port using 246 model solutions performed in 1.451 s Weighting: none diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index de36532f..e58ce305 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 0.9.42 +mkin_long_to_wide. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkin_wide_to_long. mkin 0.9.42

mkin_wide_to_long. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkinds. mkin 0.9.42

mkinds. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkinerrmin. mkin 0.9.42

mkinerrmin. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkinfit. mkin 0.9.42

mkinfit. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkin version: 0.9.42 +

mkin version: 0.9.43 R version: 3.2.4 -Date of fit: Wed Mar 23 18:10:46 2016 -Date of summary: Wed Mar 23 18:10:46 2016 +Date of fit: Thu Mar 24 08:26:29 2016 +Date of summary: Thu Mar 24 08:26:29 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 0.191 s +Fitted with method Port using 64 model solutions performed in 0.205 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 - 1.204 1.280 0.942 + 1.200 1.252 0.926

coef(fit)

diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index b3a396b9..0a361956 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9.42 +mkinmod. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkinparplot. mkin 0.9.42

mkinparplot. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkinplot. mkin 0.9.42

mkinplot. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkinpredict. mkin 0.9.42

mkinpredict. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

user system elapsed - 0.004 0.024 0.004 + 0.008 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), @@ -315,7 +315,7 @@ 201 20 4.978707 27.46227

user system elapsed - 0.016 0.004 0.002 + 0.008 0.012 0.003

system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -326,7 +326,7 @@ 201 20 4.978707 27.46227

user system elapsed - 0.048 0.008 0.055 + 0.056 0.000 0.052

diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index 5a2388dc..b5f32633 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9.42 +mkinresplot. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mkinsub. mkin 0.9.42

mkinsub. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

mmkin. mkin 0.9.42

mmkin. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

plot.mkinfit. mkin 0.9.42

plot.mkinfit. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

plot.mmkin. mkin 0.9.42

plot.mmkin. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

print.mkinds. mkin 0.9.42

print.mkinds. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

print.mkinmod. mkin 0.9.42

print.mkinmod. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

schaefer07_complex_case. mkin 0.9.42

schaefer07_complex_case. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

summary.mkinfit. mkin 0.9.42

summary.mkinfit. mkin 0.9.43

- mkin 0.9.42 + mkin 0.9.43

Index

Examples

  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
 
-mkin version:    0.9.42 
+mkin version:    0.9.43 
 R version:       3.2.4 
-Date of fit:     Wed Mar 23 18:10:56 2016 
-Date of summary: Wed Mar 23 18:10:56 2016 
+Date of fit:     Thu Mar 24 08:26:38 2016 
+Date of summary: Thu Mar 24 08:26:38 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 35 model solutions performed in 0.109 s
+Fitted with method Port using 35 model solutions performed in 0.099 s
 
 Weighting: none
 
diff --git a/inst/web/synthetic_data_for_UBA.html b/inst/web/synthetic_data_for_UBA.html
index 9fb9d23e..56a646c1 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 0.9.42
+synthetic_data_for_UBA_2014. mkin 0.9.43
 
 
 
@@ -32,7 +32,7 @@
     
   
     
-      mkin 0.9.42
+      mkin 0.9.43
       
         
            Index
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index 34428004..5e16551f 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -2,7 +2,7 @@
 
   
     
-transform_odeparms. mkin 0.9.42
+transform_odeparms. mkin 0.9.43
 
 
   
     
-      mkin 0.9.42
+      mkin 0.9.43
       
         
            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:    0.9.42 
+mkin version:    0.9.43 
 R version:       3.2.4 
-Date of fit:     Wed Mar 23 18:10:57 2016 
-Date of summary: Wed Mar 23 18:10:57 2016 
+Date of fit:     Thu Mar 24 08:26:40 2016 
+Date of summary: Thu Mar 24 08:26:40 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -144,7 +144,7 @@ d_m1 = + k_parent_m1 * parent - k_m1_sink * m1
 
 Model predictions using solution type deSolve 
 
-Fitted with method Port using 153 model solutions performed in 0.669 s
+Fitted with method Port using 153 model solutions performed in 0.662 s
 
 Weighting: none
 
diff --git a/vignettes/compiled_models.Rmd b/vignettes/compiled_models.Rmd
index 8f6df55d..c668c5fd 100644
--- a/vignettes/compiled_models.Rmd
+++ b/vignettes/compiled_models.Rmd
@@ -55,7 +55,7 @@ mb.1 <- microbenchmark(
                                solution_type = "eigen", quiet = TRUE),
   "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
                                 solution_type = "deSolve", quiet = TRUE),
-  times = 3, control = list(warmup = 1))
+  times = 3, control = list(warmup = 0))
 
 smb.1 <- summary(mb.1)
 print(mb.1)
@@ -86,7 +86,7 @@ mb.2 <- microbenchmark(
   "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, 
                                     use_compiled = FALSE, quiet = TRUE),
   "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
-  times = 3, control = list(warmup = 1))
+  times = 3, control = list(warmup = 0))
 smb.2 <- summary(mb.2)
 print(mb.2)
 smb.2["median"]/smb.2["deSolve, compiled", "median"]
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 756a2753..3215a386 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -1,94 +1,246 @@
 
+
+
+
 
-
+Benchmark for a model that can also be solved with Eigenvalues
 
-
+
 
-
-
-
+
+
-
-
-
+
+
 
 
 
-
 
-
+
-
 
 
-
-Performance benefit by using compiled model definitions in mkin
-Johannes Ranke
-2016-03-23
-
 
-
-
-Benchmark for a model that can also be solved with Eigenvalues
-Benchmark for a model that can not be solved with Eigenvalues
-
-
+
 
-
+
 Benchmark for a model that can also be solved with Eigenvalues
-This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The mkinmod() function checks for presence of the gcc compiler using
-Sys.which("gcc")
+
+This evaluation is taken from the example section of mkinfit. When using an mkin version
+equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see
+a message that the model is being compiled from autogenerated C code when
+defining a model using mkinmod. The mkinmod() function checks for presence of
+the gcc compiler using 
+
+Sys.which("gcc")
+
+
 ##            gcc 
-## "/usr/bin/gcc"
+## "/usr/bin/gcc"
+

First, we build a simple degradation model for a parent compound with one metabolite.

library("mkin")
-SFO_SFO <- mkinmod(
+
+library("mkin")
+
+
+## Loading required package: minpack.lm
+## Loading required package: rootSolve
+## Loading required package: inline
+## Loading required package: methods
+## Loading required package: parallel
+
+
+SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-## Successfully compiled differential equation model from auto-generated C code.
-We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the microbenchmark package.
-library("microbenchmark")
+  m1 = mkinsub("SFO"))
+
+
+## Successfully compiled differential equation model from auto-generated C code.
+
+
+We can compare the performance of the Eigenvalue based solution against the
+compiled version and the R implementation of the differential equations using
+the microbenchmark package.
+
+library("microbenchmark")
 library("ggplot2")
 mb.1 <- microbenchmark(
   "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
@@ -98,76 +250,115 @@ mb.1 <- microbenchmark(
                                solution_type = "eigen", quiet = TRUE),
   "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
                                 solution_type = "deSolve", quiet = TRUE),
-  times = 3, control = list(warmup = 1))
+  times = 3, control = list(warmup = 0))
+
+
+## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(SFO_SFO,
+## FOCUS_2006_D, : Could not measure overhead. Your clock might lack
+## precision.
+
+
+smb.1 <- summary(mb.1)
+print(mb.1)
+
 
-smb.1 <- summary(mb.1)
-print(mb.1)

## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 9539.3064 9543.1547 9554.1987 9547.0031 9561.6448
-##       Eigenvalue based  927.5569  928.1716  943.8293  928.7864  951.9656
-##      deSolve, compiled  734.6125  737.3273  739.0161  740.0420  741.2179
+##  deSolve, not compiled 4652.4576 4653.2263 4673.1220 4653.9950 4683.4543
+##       Eigenvalue based  749.7771  750.1327  764.7881  750.4882  772.2936
+##      deSolve, compiled  641.9152  647.6028  651.6533  653.2904  656.5223
 ##        max neval cld
-##  9576.2865     3   c
-##   975.1447     3  b 
-##   742.3938     3 a

autoplot(mb.1)

We see that using the compiled model is by a factor of 12.9 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 12.900624
-## Eigenvalue based       1.255046
-## deSolve, compiled      1.000000

+## 4712.9136 3 c +## 794.0990 3 b +## 659.7542 3 a + + +

autoplot(mb.1)
+

+ +

plot of chunk benchmark_SFO_SFO

+ +

We see that using the compiled model is by a factor of +7.1 +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 7.123930
+## Eigenvalue based      1.148782
+## deSolve, compiled     1.000000
+

Benchmark for a model that can not be solved with Eigenvalues

This evaluation is also taken from the example section of mkinfit.

FOMC_SFO <- mkinmod(
+
+This evaluation is also taken from the example section of mkinfit. 
+
+FOMC_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub( "SFO"))
-## Successfully compiled differential equation model from auto-generated C code.
-mb.2 <- microbenchmark(
+  m1 = mkinsub( "SFO"))
+
+
+## Successfully compiled differential equation model from auto-generated C code.
+
+
+mb.2 <- microbenchmark(
   "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, 
                                     use_compiled = FALSE, quiet = TRUE),
   "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
-  times = 3, control = list(warmup = 1))
-smb.2 <- summary(mb.2)
-print(mb.2)
+  times = 3, control = list(warmup = 0))
+

+ +

## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(FOMC_SFO,
+## FOCUS_2006_D, : Could not measure overhead. Your clock might lack
+## precision.
+

+ +

smb.2 <- summary(mb.2)
+print(mb.2)
+

## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 20.728228 20.867978 20.959811 21.007729 21.075602
-##      deSolve, compiled  1.343219  1.382365  1.399697  1.421511  1.427936
+##  deSolve, not compiled 10.202245 10.243829 10.260112 10.285413 10.289045
+##      deSolve, compiled  1.176863  1.182699  1.188555  1.188536  1.194402
 ##        max neval cld
-##  21.143476     3   b
-##   1.434362     3  a

smb.2["median"]/smb.2["deSolve, compiled", "median"]

+## 10.292677 3 b +## 1.200267 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 14.8 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.42 on

## R version 3.2.4 Revised (2016-03-16 r70336)
-## Platform: x86_64-pc-linux-gnu (64-bit)
-## Running under: Debian GNU/Linux 8 (jessie)

## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz

+## 2 NA + +

autoplot(mb.2)
+

- +

## R Under development (unstable) (2016-03-23 r70368)
+## Platform: x86_64-pc-linux-gnu (64-bit)
+## Running under: Debian GNU/Linux 8 (jessie)
+

## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz
+

+ -- cgit v1.2.1