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-rw-r--r--DESCRIPTION4
-rw-r--r--NEWS.md2
-rw-r--r--R/create_deg_func.R24
-rw-r--r--build.log2
-rw-r--r--check.log5
-rw-r--r--docs/404.html2
-rw-r--r--docs/articles/index.html2
-rw-r--r--docs/authors.html2
-rw-r--r--docs/index.html2
-rw-r--r--docs/news/index.html3
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/create_deg_func.html16
-rw-r--r--docs/reference/index.html2
-rw-r--r--man/create_deg_func.Rd9
-rw-r--r--test.log16
-rw-r--r--tests/testthat/setup_script.R11
-rw-r--r--tests/testthat/test_analytical.R14
17 files changed, 88 insertions, 30 deletions
diff --git a/DESCRIPTION b/DESCRIPTION
index 5f38d12c..0facf77e 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,8 +1,8 @@
Package: mkin
Type: Package
Title: Kinetic Evaluation of Chemical Degradation Data
-Version: 0.9.50
-Date: 2020-05-07
+Version: 0.9.50.1
+Date: 2020-05-11
Authors@R: c(person("Johannes", "Ranke", role = c("aut", "cre", "cph"),
email = "jranke@uni-bremen.de",
comment = c(ORCID = "0000-0003-4371-6538")),
diff --git a/NEWS.md b/NEWS.md
index 2512f361..49828447 100644
--- a/NEWS.md
+++ b/NEWS.md
@@ -4,6 +4,8 @@
- 'mkinmod': Make 'use_of_ff' = "max" the default
+- Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO
+
# mkin 0.9.49.11 (2020-04-20)
- Increase a test tolerance to make it pass on all CRAN check machines
diff --git a/R/create_deg_func.R b/R/create_deg_func.R
index 11559799..b29a11f7 100644
--- a/R/create_deg_func.R
+++ b/R/create_deg_func.R
@@ -16,7 +16,14 @@
#' benchmark(
#' analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
#' deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
-#' replications = 1)
+#' replications = 2)
+#' DFOP_SFO <- mkinmod(
+#' parent = mkinsub("DFOP", "m1"),
+#' m1 = mkinsub("SFO"))
+#' benchmark(
+#' analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
+#' deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
+#' replications = 2)
#' }
create_deg_func <- function(spec, use_of_ff = c("min", "max")) {
@@ -94,6 +101,21 @@ create_deg_func <- function(spec, use_of_ff = c("min", "max")) {
"(((", k2, "-", k12, "-", k10, ")*", n20, "-", k12, "*", n10, ")*exp(-", k2, "*t)+",
k12, "*", n10, "*exp(-(", k_parent, ")*t))/(", k2, "-(", k_parent, "))")
}
+
+ # dfop_f12_sfo
+ if (all(use_of_ff == "max", spec[[1]]$sink == TRUE, length(obs_vars) == 2,
+ spec[[1]]$type == "DFOP", spec[[2]]$type == "SFO")) {
+ supported <- TRUE
+ f12 <- paste0("f_", n1, "_to_", n2)
+ k2 <- paste0("k_", n2)
+ predicted_text[n2] <- paste0(
+ "((", f12, "* g - ", f12, ") * k2 * ", n10, " * exp(- k2 * t))/(k2 - ", k2, ") - ",
+ "((", f12, "* g) * k1 * ", n10, " * exp(- k1 * t))/(k1 - ", k2, ") + ",
+ "(((k1 - ", k2, ") * k2 - ", k2, "* k1 + ", k2, "^2) * ", n20, "+",
+ "((", f12, "* k1 + (", f12, "*g - ", f12, ") * ", k2, ") * k2 - ", f12, " * g * ", k2, " * k1) * ", n10, ") * ",
+ "exp( - ", k2, " * t)/((k1 - ", k2, ") * k2 - ", k2, " * k1 + ", k2, "^2)")
+ }
+
}
diff --git a/build.log b/build.log
index b3df3235..4c64021a 100644
--- a/build.log
+++ b/build.log
@@ -5,5 +5,5 @@
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
-* building ‘mkin_0.9.50.tar.gz’
+* building ‘mkin_0.9.50.1.tar.gz’
diff --git a/check.log b/check.log
index 8064f9a6..99cb6f86 100644
--- a/check.log
+++ b/check.log
@@ -1,11 +1,11 @@
* using log directory ‘/home/jranke/git/mkin/mkin.Rcheck’
-* using R Under development (unstable) (2020-05-10 r78402)
+* using R version 4.0.0 (2020-04-24)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using options ‘--no-tests --as-cran’
* checking for file ‘mkin/DESCRIPTION’ ... OK
* checking extension type ... Package
-* this is package ‘mkin’ version ‘0.9.50’
+* this is package ‘mkin’ version ‘0.9.50.1’
* package encoding: UTF-8
* checking CRAN incoming feasibility ... Note_to_CRAN_maintainers
Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
@@ -35,6 +35,7 @@ Maintainer: ‘Johannes Ranke <jranke@uni-bremen.de>’
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
+* checking loading without being on the library search path ... OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
diff --git a/docs/404.html b/docs/404.html
index c6da911d..afb82b3f 100644
--- a/docs/404.html
+++ b/docs/404.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="https://pkgdown.jrwb.de/mkin/index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/articles/index.html b/docs/articles/index.html
index 7091d4c9..5179c1bc 100644
--- a/docs/articles/index.html
+++ b/docs/articles/index.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/authors.html b/docs/authors.html
index bc170e49..5ec134d6 100644
--- a/docs/authors.html
+++ b/docs/authors.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/index.html b/docs/index.html
index 5c4a0a9b..37ed972a 100644
--- a/docs/index.html
+++ b/docs/index.html
@@ -37,7 +37,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/docs/news/index.html b/docs/news/index.html
index 1e13041d..3965df70 100644
--- a/docs/news/index.html
+++ b/docs/news/index.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
@@ -145,6 +145,7 @@
<ul>
<li><p>Support SFORB with formation fractions</p></li>
<li><p>‘mkinmod’: Make ‘use_of_ff’ = “max” the default</p></li>
+<li><p>Improve performance by a) avoiding expensive calls in the cost function like merge() and data.frame(), and b) by implementing analytical solutions for SFO-SFO and DFOP-SFO</p></li>
</ul>
</div>
<div id="mkin-0-9-49-11-2020-04-20" class="section level1">
diff --git a/docs/pkgdown.yml b/docs/pkgdown.yml
index b3cd3d30..aa796e47 100644
--- a/docs/pkgdown.yml
+++ b/docs/pkgdown.yml
@@ -10,7 +10,7 @@ articles:
NAFTA_examples: web_only/NAFTA_examples.html
benchmarks: web_only/benchmarks.html
compiled_models: web_only/compiled_models.html
-last_built: 2020-05-11T03:18Z
+last_built: 2020-05-11T13:20Z
urls:
reference: https://pkgdown.jrwb.de/mkin/reference
article: https://pkgdown.jrwb.de/mkin/articles
diff --git a/docs/reference/create_deg_func.html b/docs/reference/create_deg_func.html
index 67016be0..6d05e811 100644
--- a/docs/reference/create_deg_func.html
+++ b/docs/reference/create_deg_func.html
@@ -175,9 +175,19 @@
<span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(
<span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
<span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>SFO_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
- <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>1</span>)</div><div class='output co'>#&gt; <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
-#&gt; 1 analytical 1 0.198 1.000 0.198 0.000 0
-#&gt; 2 deSolve 1 0.350 1.768 0.348 0.001 0
+ <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#&gt; <span class='message'>Lade nötiges Paket: rbenchmark</span></div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
+#&gt; 1 analytical 2 0.395 1.000 0.393 0.002 0
+#&gt; 2 deSolve 2 0.693 1.754 0.692 0.000 0
+#&gt; sys.child
+#&gt; 1 0
+#&gt; 2 0</div><div class='input'> <span class='no'>DFOP_SFO</span> <span class='kw'>&lt;-</span> <span class='fu'><a href='mkinmod.html'>mkinmod</a></span>(
+ <span class='kw'>parent</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"DFOP"</span>, <span class='st'>"m1"</span>),
+ <span class='kw'>m1</span> <span class='kw'>=</span> <span class='fu'><a href='mkinsub.html'>mkinsub</a></span>(<span class='st'>"SFO"</span>))</div><div class='output co'>#&gt; <span class='message'>Successfully compiled differential equation model from auto-generated C code.</span></div><div class='input'> <span class='fu'><a href='https://rdrr.io/pkg/rbenchmark/man/benchmark.html'>benchmark</a></span>(
+ <span class='kw'>analytical</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>DFOP_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"analytical"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
+ <span class='kw'>deSolve</span> <span class='kw'>=</span> <span class='fu'><a href='mkinfit.html'>mkinfit</a></span>(<span class='no'>DFOP_SFO</span>, <span class='no'>FOCUS_D</span>, <span class='kw'>solution_type</span> <span class='kw'>=</span> <span class='st'>"deSolve"</span>, <span class='kw'>quiet</span> <span class='kw'>=</span> <span class='fl'>TRUE</span>),
+ <span class='kw'>replications</span> <span class='kw'>=</span> <span class='fl'>2</span>)</div><div class='output co'>#&gt; test replications elapsed relative user.self sys.self user.child
+#&gt; 1 analytical 2 0.870 1.000 0.870 0 0
+#&gt; 2 deSolve 2 1.678 1.929 1.677 0 0
#&gt; sys.child
#&gt; 1 0
#&gt; 2 0</div><div class='input'># }
diff --git a/docs/reference/index.html b/docs/reference/index.html
index 7e7fff29..ed6debdd 100644
--- a/docs/reference/index.html
+++ b/docs/reference/index.html
@@ -71,7 +71,7 @@
</button>
<span class="navbar-brand">
<a class="navbar-link" href="../index.html">mkin</a>
- <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50</span>
+ <span class="version label label-default" data-toggle="tooltip" data-placement="bottom" title="Released version">0.9.50.1</span>
</span>
</div>
diff --git a/man/create_deg_func.Rd b/man/create_deg_func.Rd
index 178661ff..69058038 100644
--- a/man/create_deg_func.Rd
+++ b/man/create_deg_func.Rd
@@ -30,6 +30,13 @@ if (require(rbenchmark))
benchmark(
analytical = mkinfit(SFO_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
deSolve = mkinfit(SFO_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
- replications = 1)
+ replications = 2)
+ DFOP_SFO <- mkinmod(
+ parent = mkinsub("DFOP", "m1"),
+ m1 = mkinsub("SFO"))
+ benchmark(
+ analytical = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "analytical", quiet = TRUE),
+ deSolve = mkinfit(DFOP_SFO, FOCUS_D, solution_type = "deSolve", quiet = TRUE),
+ replications = 2)
}
}
diff --git a/test.log b/test.log
index f2f9ff85..54f61d9b 100644
--- a/test.log
+++ b/test.log
@@ -4,19 +4,19 @@ Testing mkin
✔ | 2 | Export dataset for reading into CAKE
✔ | 13 | Results for FOCUS D established in expertise for UBA (Ranke 2014) [1.1 s]
✔ | 4 | Calculation of FOCUS chi2 error levels [0.4 s]
-✔ | 7 | Fitting the SFORB model [3.4 s]
-✔ | 4 | Analytical solutions for coupled models [1.7 s]
+✔ | 7 | Fitting the SFORB model [3.2 s]
+✔ | 5 | Analytical solutions for coupled models [3.0 s]
✔ | 5 | Calculation of Akaike weights
✔ | 10 | Confidence intervals and p-values [1.0 s]
-✔ | 14 | Error model fitting [4.0 s]
+✔ | 14 | Error model fitting [3.8 s]
✔ | 4 | Test fitting the decline of metabolites from their maximum [0.2 s]
✔ | 1 | Fitting the logistic model [0.2 s]
✔ | 1 | Test dataset class mkinds used in gmkin
✔ | 12 | Special cases of mkinfit calls [0.6 s]
✔ | 8 | mkinmod model generation and printing [0.2 s]
-✔ | 3 | Model predictions with mkinpredict [0.4 s]
+✔ | 3 | Model predictions with mkinpredict [0.3 s]
✔ | 16 | Evaluations according to 2015 NAFTA guidance [1.4 s]
-✔ | 9 | Nonlinear mixed-effects models [7.6 s]
+✔ | 9 | Nonlinear mixed-effects models [7.5 s]
✔ | 4 | Calculation of maximum time weighted average concentrations (TWAs) [2.4 s]
✔ | 3 | Summary
✔ | 14 | Plotting [1.4 s]
@@ -24,13 +24,13 @@ Testing mkin
✔ | 4 | Residuals extracted from mkinfit models
✔ | 2 | Complex test case from Schaefer et al. (2007) Piacenza paper [1.4 s]
✔ | 1 | Summaries of old mkinfit objects
-✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.3 s]
+✔ | 4 | Results for synthetic data established in expertise for UBA (Ranke 2014) [2.4 s]
✔ | 9 | Hypothesis tests [6.5 s]
══ Results ═════════════════════════════════════════════════════════════════════
-Duration: 36.4 s
+Duration: 37.3 s
-OK: 158
+OK: 159
Failed: 0
Warnings: 0
Skipped: 0
diff --git a/tests/testthat/setup_script.R b/tests/testthat/setup_script.R
index 58e328cd..def52697 100644
--- a/tests/testthat/setup_script.R
+++ b/tests/testthat/setup_script.R
@@ -40,16 +40,19 @@ fits <- mmkin(models,
# One metabolite
SFO_SFO <- mkinmod(parent = mkinsub("SFO", to = "m1"),
- m1 = mkinsub("SFO"),
- use_of_ff = "min", quiet = TRUE)
+ m1 = mkinsub("SFO"),
+ use_of_ff = "min", quiet = TRUE)
SFO_SFO.ff <- mkinmod(parent = mkinsub("SFO", to = "m1"),
- m1 = mkinsub("SFO"),
- use_of_ff = "max", quiet = TRUE)
+ m1 = mkinsub("SFO"),
+ use_of_ff = "max", quiet = TRUE)
SFO_SFO.ff.nosink <- mkinmod(
parent = mkinsub("SFO", "m1", sink = FALSE),
m1 = mkinsub("SFO"), quiet = TRUE, use_of_ff = "max")
FOMC_SFO <- mkinmod(parent = mkinsub("FOMC", to = "m1"),
m1 = mkinsub("SFO"), quiet = TRUE)
+DFOP_SFO <- mkinmod(parent = mkinsub("DFOP", to = "m1"),
+ m1 = mkinsub("SFO"),
+ use_of_ff = "max", quiet = TRUE)
# Avoid warning when fitting a dataset where zero value is removed
FOCUS_D <- subset(FOCUS_2006_D, value != 0)
diff --git a/tests/testthat/test_analytical.R b/tests/testthat/test_analytical.R
index 5972a18a..578258d3 100644
--- a/tests/testthat/test_analytical.R
+++ b/tests/testthat/test_analytical.R
@@ -1,6 +1,6 @@
context("Analytical solutions for coupled models")
-test_that("The analytical solutions of SFO-SFO are correct", {
+test_that("The analytical solutions for SFO-SFO are correct", {
# No sink, no formation fractions
SFO_SFO_nosink <- mkinmod(
parent = mkinsub("SFO", to = "m1", sink = FALSE),
@@ -44,3 +44,15 @@ test_that("The analytical solutions of SFO-SFO are correct", {
)
})
+
+test_that("The analytical solution for DFOP-SFO are correct", {
+ # With formation fraction
+ f_dfop_sfo_analytical <- mkinfit(DFOP_SFO, FOCUS_D,
+ solution_type = "analytical", quiet = TRUE)
+ f_dfop_sfo_desolve <- mkinfit(DFOP_SFO, FOCUS_D,
+ solution_type = "deSolve", quiet = TRUE)
+ expect_equal(
+ parms(f_dfop_sfo_analytical),
+ parms(f_dfop_sfo_desolve)
+ )
+})

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