Add analytical solution for DFOP-SFO

This is about twice as fast as deSolve compiled in the case of FOCUS D

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)
+  )
+})