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---
title: "Performance benefit by using compiled model definitions in mkin"
output:
html_document:
css: mkin_vignettes.css
toc: true
mathjax: null
theme: united
---
<!--
%\VignetteEngine{knitr::rmarkdown}
%\VignetteIndexEntry{Performance benefit by using compiled model definitions in mkin}
-->
```{r, include = FALSE}
library(knitr)
opts_chunk$set(tidy = FALSE, cache = TRUE)
if (!require("ccSolve"))
message("Please install the ccSolve package for this vignette to produce sensible output")
```
# 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
greater than 0.9-36 and the ccSolve package is installed and functional, you will get a
message that the model is being compiled when defining a model using mkinmod.
```{r create_SFO_SFO}
library("mkin")
SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1", sink = TRUE),
m1 = list(type = "SFO"))
```
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.
```{r benchmark_SFO_SFO, echo=-(1:2)}
# Redefining the model, in order not to confuse the knitr cache which leads to segfaults
suppressMessages(SFO_SFO <- mkinmod(
parent = list(type = "SFO", to = "m1", sink = TRUE),
m1 = list(type = "SFO")))
library("microbenchmark")
mb.1 <- microbenchmark(
mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", use_compiled = FALSE,
quiet = TRUE),
mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE),
mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "deSolve", quiet = TRUE),
times = 3, control = list(warmup = 1))
smb.1 <- summary(mb.1)[-1]
rownames(smb.1) <- c("deSolve, not compiled", "Eigenvalue based", "deSolve, compiled")
print(smb.1)
```
We see that using the compiled model is almost a factor of 8 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:
```{r}
smb.1["median"]/smb.1["deSolve, compiled", "median"]
```
# Benchmark for a model that can not be solved with Eigenvalues
This evaluation is also taken from the example section of mkinfit.
```{r benchmark_FOMC_SFO}
FOMC_SFO <- mkinmod(
parent = list(type = "FOMC", to = "m1", sink = TRUE),
m1 = list(type = "SFO"))
mb.2 <- microbenchmark(
mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE),
mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
times = 3, control = list(warmup = 1))
smb.2 <- summary(mb.2)[-1]
rownames(smb.2) <- c("deSolve, not compiled", "deSolve, compiled")
print(smb.2)
smb.2["median"]/smb.2["deSolve, compiled", "median"]
```
Here we get a performance benefit of more than a factor of 8 using the version
of the differential equation model compiled from C code using the ccSolve package!
|
