From 47ba9ea512b82fb8b31da8ec5558f3c0952d86d4 Mon Sep 17 00:00:00 2001 From: Johannes Ranke Date: Thu, 2 Apr 2020 10:58:34 +0200 Subject: Compiled models article, reduce distractions - Added a section with platform specific notes on getting compiled models to work to the compiled models article - Don't return empty SFORB parameter list from endpoints() if there is no SFORB model - Avoid warnings when using standardized = TRUE in plot.mmkin() --- docs/articles/web_only/compiled_models.html | 171 ++++++++++------------------ docs/news/index.html | 17 ++- docs/reference/endpoints.html | 5 +- docs/reference/plot.mmkin.html | 7 ++ 4 files changed, 85 insertions(+), 115 deletions(-) (limited to 'docs') diff --git a/docs/articles/web_only/compiled_models.html b/docs/articles/web_only/compiled_models.html index 363f0c38..6daabd5e 100644 --- a/docs/articles/web_only/compiled_models.html +++ b/docs/articles/web_only/compiled_models.html @@ -31,7 +31,7 @@ mkin - 0.9.49.6 + 0.9.49.9 @@ -90,7 +90,7 @@

Performance benefit by using compiled model definitions in mkin

Johannes Ranke

-

2019-11-01

+

2020-04-02

@@ -99,75 +99,49 @@ -
+

-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")
-
##            gcc 
-## "/usr/bin/gcc"
+How to benefit from compiled models +

When using an mkin version equal to or greater than 0.9-36 and a C compiler is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. Starting from version 0.9.49.9, the mkinmod() function checks for presence of a compiler using

+ +

In previous versions, it used Sys.which("gcc") for this check.

+

On Linux, you need to have the essential build tools like make and gcc or clang installed. On Debian based linux distributions, these will be pulled in by installing the build-essential package.

+

On MacOS, which I do not use personally, I have had reports that a compiler is available by default.

+

On Windows, you need to install Rtools and have the path to its bin directory in your PATH variable. You do not need to modify the PATH variable when installing Rtools. Instead, I would recommend to put the line

+
Sys.setenv(PATH = paste("C:/Rtools/bin", Sys.getenv("PATH"), sep=";"))
+

into your .Rprofile startup file. This is just a text file with some R code that is executed when your R session starts. It has to be named .Rprofile and has to be located in your home directory, which will generally be your Documents folder. You can check the location of the home directory used by R by issuing

+
Sys.getenv("HOME")
+
+
+

+Comparison with Eigenvalue based solutions

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

-
library("mkin", quietly = TRUE)
-SFO_SFO <- mkinmod(
-  parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
+
library("mkin", quietly = TRUE)
+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 benchmark package.

- -
## Lade nötiges Paket: rbenchmark
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve",
-## use_compiled = FALSE, : Observations with value of zero were removed from
-## the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet =
-## TRUE): Observations with value of zero were removed from the data
-
## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet
-## = TRUE): Observations with value of zero were removed from the data
+

We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the benchmark package. In the output of below code, the warnings about zero being removed from the FOCUS D dataset are suppressed.

+ 
##                    test replications elapsed relative user.self sys.self
-## 3     deSolve, compiled            3   3.143    1.000     3.142        0
-## 1 deSolve, not compiled            3  29.169    9.281    29.154        0
-## 2      Eigenvalue based            3   4.358    1.387     4.356        0
+## 3     deSolve, compiled            3   3.239    1.000     3.237        0
+## 1 deSolve, not compiled            3  29.758    9.187    29.739        0
+## 2      Eigenvalue based            3   4.558    1.407     4.554        0
 ##   user.child sys.child
 ## 3          0         0
 ## 1          0         0
@@ -178,52 +152,32 @@
 

 Model that can not be solved with Eigenvalues

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

-
if (require(rbenchmark)) {
-  FOMC_SFO <- mkinmod(
-    parent = mkinsub("FOMC", "m1"),
-    m1 = mkinsub( "SFO"))
-
-  b.2 <- benchmark(
-    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
-                                      use_compiled = FALSE, quiet = TRUE),
-    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
-    replications = 3)
-  print(b.2)
-  factor_FOMC_SFO <- round(b.2["1", "relative"])
-} else {
-  factor_FOMC_SFO <- NA
-  print("R package benchmark is not available")
-}

+
if (require(rbenchmark)) {
+  FOMC_SFO <- mkinmod(
+    parent = mkinsub("FOMC", "m1"),
+    m1 = mkinsub( "SFO"))
+
+  b.2 <- benchmark(
+    "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D,
+                                      use_compiled = FALSE, quiet = TRUE),
+    "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
+    replications = 3)
+  print(b.2)
+  factor_FOMC_SFO <- round(b.2["1", "relative"])
+} else {
+  factor_FOMC_SFO <- NA
+  print("R package benchmark is not available")
+}

 
## Successfully compiled differential equation model from auto-generated C code.

-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data

-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data

-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet =
-## TRUE): Observations with value of zero were removed from the data

-
## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data
-
-## Warning in mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE): Observations with
-## value of zero were removed from the data

 
##                    test replications elapsed relative user.self sys.self
-## 2     deSolve, compiled            3   4.840    1.000     4.837        0
-## 1 deSolve, not compiled            3  54.338   11.227    54.309        0
+## 2     deSolve, compiled            3   4.984    1.000     4.981    0.000
+## 1 deSolve, not compiled            3  55.358   11.107    55.326    0.003
 ##   user.child sys.child
 ## 2          0         0
 ## 1          0         0

 
Here we get a performance benefit of a factor of 11 using the version of the differential equation model compiled from C code!

-
This vignette was built with mkin 0.9.49.6 on

-
## R version 3.6.1 (2019-07-05)
+
This vignette was built with mkin 0.9.49.9 on

+
## R version 3.6.3 (2020-02-29)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
 ## Running under: Debian GNU/Linux 10 (buster)

 
## CPU model: AMD Ryzen 7 1700 Eight-Core Processor

@@ -236,7 +190,8 @@
       

 Contents
diff --git a/docs/news/index.html b/docs/news/index.html index c2b5865f..fc9a0765 100644 --- a/docs/news/index.html +++ b/docs/news/index.html @@ -129,9 +129,19 @@
-
+

-mkin 0.9.49.9 (unreleased) Unreleased +mkin 0.9.49.10 (unreleased) Unreleased +

+
    +

  • ‘endpoints’: Don’t return the SFORB list component if it’s empty. This reduces distraction and complies with the documentation

    • +

  • Article in compiled models: Add some platform specific code and suppress warnings about zero values being removed from the FOCUS D dataset

    • +

  • ‘plot.mmkin’: Add the argument ‘standardized’ to avoid warnings that occurred when it was passed as part of the additional arguments captured by the dots (…)

    • +
+
+
+

+mkin 0.9.49.9 (2020-03-31) 2020-03-31

  • ‘mkinmod’: Use pkgbuild::has_compiler instead of Sys.which(‘gcc’), as the latter will often fail even if Rtools are installed

    • @@ -756,7 +766,8 @@

    Contents

      -
    • 0.9.49.9
      • +
    • 0.9.49.10
      • +
    • 0.9.49.9
    • 0.9.49.8
    • 0.9.49.7
    • 0.9.49.6
      • diff --git a/docs/reference/endpoints.html b/docs/reference/endpoints.html index e81bdbb5..f201294d 100644 --- a/docs/reference/endpoints.html +++ b/docs/reference/endpoints.html @@ -75,7 +75,7 @@ advantage that the SFORB model can also be used for metabolites." /> mkin - 0.9.49.6 + 0.9.49.9
    @@ -171,9 +171,6 @@ advantage that the SFORB model can also be used for metabolites.

    endpoints(fit)
#> $ff #> logical(0) #> -#> $SFORB -#> logical(0) -#> #> $distimes #> DT50 DT90 DT50back #> parent 1.785233 15.1479 4.559973 diff --git a/docs/reference/plot.mmkin.html b/docs/reference/plot.mmkin.html index 9d41b4c1..be60f228 100644 --- a/docs/reference/plot.mmkin.html +++ b/docs/reference/plot.mmkin.html @@ -149,6 +149,7 @@ the fit of at least one model to the same dataset is shown.

main = "auto", legends = 1, resplot = c("time", "errmod"), + standardized = FALSE, show_errmin = TRUE, errmin_var = "All data", errmin_digits = 3, @@ -179,6 +180,12 @@ column.

Should the residuals plotted against time, using mkinresplot, or as squared residuals against predicted values, with the error model, using mkinerrplot.

+ + + standardized +

Should the residuals be standardized? This option +is passed to mkinresplot, it only takes effect if +`resplot = "time"`.

show_errmin -- cgit v1.2.1