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-rw-r--r--R/create_deg_func.R24
-rw-r--r--docs/pkgdown.yml2
-rw-r--r--docs/reference/create_deg_func.html16
-rw-r--r--man/create_deg_func.Rd9
-rw-r--r--tests/testthat/setup_script.R11
-rw-r--r--tests/testthat/test_analytical.R14
6 files changed, 65 insertions, 11 deletions
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/docs/pkgdown.yml b/docs/pkgdown.yml
index b3cd3d30..814bf679 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: 2020-05-11T13:00Z
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/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/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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